Laboratory Informatics Guide 2021 Understanding the needs of the laboratory
From the publishers of SCIENTIFIC COMPUTING WORLD www.scientific-computing.com/lig21 Transform Digital Lab Consulting® provides independent strategic consulting to enable organisations of all sizes to transform their business through better use of informatics.
We provide clear, actionable advice to help companies find the most effective solution for their environment.
We have over 20 years of experience across the entire value chain, from early research to manufacturing.
We are based in the UK and work globally with our clients and partners.
Discover more at dlc.io
+44 (0)1543 547607 [email protected] LABWARE LIMS and ELN in a single platform Automation software for all laboratories
Offices worldwide supporting customers in more than 125 countries
www.labware.com CDD BH EU 297x210mmV4.pdf 1 30/09/2020 11:54
CDD BH EU 297x210mmV4.pdf 1 30/09/2020 11:54
C
M
C Y
M CM
Y MY
CM CY
MY CMY
CY K
CMY
K CDD BH EU 297x210mmV4.pdf 1 30/09/2020 11:54
Contents
t is clear that Covid-19 has had a significant impact on laboratory operations. Even for laboratories that are not working directly on Covid-19 Itesting, drug and vaccine development, restrictions on laboratory space and access to equipment are putting a significant burden on scientists. Thankfully, laboratory informatics software tools can shoulder some of that burden by providing a platform for remote Software tools help combat Digitial transformation access, automation of laboratory operations 4 Covid-19 22 or by providing access to data and tools for collaboration to keep scientists working Robert Roe looks at how Covid-19 is driving Sophia Ktori looks at the role software plays in productively. changes in the laboratory transforming the laboratory This issue of the Laboratory Informatics Guide aims to highlight the working practices of researchers, and highlight Vendor predictions Looking at cancer 10 28 technologies and tools that can help overcome the challenges that scientists How laboratory technology and software could Advances in computer vision combined with AI face in the laboratory. We start with an in-
C change due to increased pressures to work computing help pathologists to more accurately depth look at the work that has been going remotely caused by the pandemic identify subtypes of cancer on around the world to fight against the M pandemic on page 4.
Y We’ve a series of vendor predictions for Making science open Empowering collaboration the year ahead beginning on page 10. Thie CM with the cloud 16 30 features experts from several informatics MY The European Bioinformatics Institute is Cloud technologies can simplify data sharing software providers discussing the role of
CY developing tools and infrastructure to promote and collaboration, writes Thermo Fisher’s Darren automation, cloud-based systems, remote open science and provide programmatic access to Barrington-Light access tools, and other technologies that CMY biological data can ensure laboratory productivity, despite K reduced access for many users. Starting on pages 16 and 20 are two Leading genomics Supplier’s directory research interviews with research leaders. The first 20 32 features the European Bioinformatics Institute and the second takes a look at the The Wellcome Sanger Institute’s Julia Wilson Our guide to find where to turn to for the Wellcome Sanger Institute. The interviews discusses the role of the research centre and its suppliers you need share some of the work that has been impact on the wider scientific community conducted on Covid-19 and the importance of open science in fighting the pandemic. Digital transformation in the laboratory is the focus on page 22, as Sophia Ktori talks SUBSCRIPTIONS: The Laboratory Informatics Guide 2021 is published EDITORIAL AND ADMINISTRATIVE TEAM to informatics software providers about the by Europa Science Ltd, which also Managing Editor: Tim Gillett publishes Scientific Computing World. ([email protected]) technologies and tools scientists can use to Free registration is available to qualifying individuals (register online at Editor: Robert Roe advance lab operations. www.scientific-computing.com). ([email protected]) On page 28 we consider how advances Subscriptions £100 a year for six issues to Feature Writer: Sophia Ktori readers outside registration requirements. Circulation/readership enquiries: in computer vision, combined with AI Single issue £20. Orders to ESL, SCW [email protected] Circulation, 4 Signet Court, Cambridge computing, are helping pathologists more CB5 8LA, UK. Tel: +44 (0)1223 221030. ADVERTISING TEAM accurately identify subtypes of cancer. And Fax: +44 (0)1223 213385. ©2020 Europa Science Ltd. Advertising Sales Manager: Mike Nelson finally, Thermo Fisher’s Darren Barrington- Whilst every care has been taken in the compilation of this magazine, ([email protected]) errors or omissions are not the responsibility of the publishers or of Tel: +44 (0) 1223 221039 Fax +44 (0) 1223 213385 Light details the importance of cloud-based the editorial staff. Opinions expressed are not necessarily those of the publishers or editorial staff. All rights reserved. Unless specifically solutions on page 30. stated, goods or services mentioned are not formally endorsed by DESIGN TEAM Europa Science Ltd, which does not guarantee or endorse or accept Production manager: David Houghton any liability for any goods and/or services featured in this publication. ([email protected]) US copies: Scientific Computing World (ISSN 1356-7853/USPS No Senior graphic designer: Zöe Andrews 018-753) is published bi-monthly for £100 per year by Europa Science ([email protected]) Ltd, and distributed in the USA by DSW, 75 Aberdeen Rd, Emigsville PA 17318-0437. Periodicals postage paid at Emigsville PA. Postmaster: CORPORATE TEAM Send address corrections to Scientific Computing World PO Box 437, Emigsville, PA 17318-0437. Managing director: Warren Clark Web: www.scientific-computing.com Cover image and all other images: Shutterstock.com
www.scientific-computing.com/lig21 3 LABORATORY INFORMATICS GUIDE 2021
Covid-19 changes the laboratory landscape
Demand for testing and requirements for remote working tools drive changes in the laboratory “The tooling and he pandemic has defined the laboratory information management development of laboratory system (LIMS) and electronic laboratory solutions, like Tsoftware and technologies, notebook (ELN) software to help the LIMS that we as collaboration and remote working manage collaborative work, and tools become requirements to a promote reduced-capacity working offer, become productive laboratory. environments in the laboratory. more pivotal and It has increased demand for Patrick Rose, digital science product laboratory services in areas such as manager at Thermo Fisher Scientific, critical” testing, genomics studies and vaccine notes that there has been a pivot in and drug development. However the tools used in laboratories due to ‘What we are seeing is an increased these demands must be met with Covid-19. ‘The labs are starting work need to work remotely due to restrictions on laboratory space and leaner, they are having to collaborate alternating days, slimmer shifts trying more demanding project timelines. with other partners, other contract to minimise the time people are in there To facilitate this research and research organisations [CROs] to together. But, they still need to work scale-up testing capabilities, help battle the pandemic and find the on their results, gather and share data laboratory scientists are using vaccine. and collaborate,’ added Rose. ‘So the
4 www.scientific-computing.com/lig21 LABORATORY INFORMATICS GUIDE 2021 tooling and solutions, like the LIMS that we offer, become more pivotal and critical. It is being able to see what “We put automated software other users have done – potentially processes in place to help capture what they may have done in the last shift, what you need to do for the next testing data: that may be challenging shift.’ because you are out in the field
Tools facilitate remote working somewhere” LIMS or ELN systems can help to minimise the time scientists have to spend in the lab, as mobile alerts or other features can help notify scientists when their experiments will patient, according to their age, sex, background. Importantly, it could also be finishing. Streamlining data sharing whether they have other diseases – feedback information to the prescribing and access also helps facilitate agile comorbidities – and other factors, and physician, so that they will know how decision making, and lets scientists thereby give guidance to clinicians on well the patient is sticking to their drug access data and analyse or work on likely optimum dosing. schedule,’ Astic suggested. data from home. Development of the drug exposure ‘Our first model, for paracetamol, Several LIMS and ELN vendors are models will leverage data held in could help dramatically reduce now equipping their software with pre- thousands of drug-related documents overuse of the drug and even prevent configured workloads to help scientists in Elsevier’s PharmaPendium drug data overdose-related deaths.’ ‘We signed get set up with key laboratory resource, which contains decades of a partnership with Vidal, a key player operations. This reduces the amount searchable FDA and EMA regulatory of medical information in France, to of setup and administrative work that approval and related documents on the integrate our technology into their needs to be done by scientists, which drugs. Vidal Sentinel platform designed should lead to increased productivity. Olivier Barberan, director of for hospitals. They call our API Lauren Taylor, digital science translational medical solutions at [Application Programming Interface] solutions manager at Thermo Fisher Elsevier explains: ‘We will provide and the pharmacist or doctor can run Scientific, said: ‘Some of those ExactCure with information held in personalised simulations until they workflows we have already pre- PharmaPendium that spans more reach what they estimate to be the best configured to get customers up and than 50 drug-specific parameters, posology for a given patient,’ added running as quickly as possible. In terms including PK and pharmacodynamic Astic. of the integration of instrumentation, data, safety data, adverse events and Digital companion apps could also for example, you may have specimens drug-drug interaction records, together be utilised by the pharma industry in the lab that you want to sequence, with data on drug efficacy. This may to support clinical drug trials and that information needs to be put onto encompass many thousands of reports, potentially speed time to market, while the sequencer so that you know which for example, there were in excess of reducing attrition at the trials stage. samples you are sequencing, and that 13,000 records just for the antiviral information can be relayed back to the drug ritonavir, which is one of the drugs Dosing optimisation for Covid-19 correct sample. under consideration for Covid-19 Certara launched the Covid-19 ‘The integration really is automating therapy.’ Pharmacology Resource Center in April, the push of information to the ExactCure is exploiting the an online resource giving scientists sequencers, so that you are not PharmaPendium data and its own AI around the world access to simulation copying and pasting or uploading and tools to build a simulation-based digital and modelling tools to aid the design downloading files manually.’ companion – a digital twin application of clinical trials and optimise dosing for smartphones that patients would regimes for candidate drugs such as Using AI in the fight against Covid-19 use to help make sure that they use hydroxychloroquine, and lopinavir/ AI tools are becoming increasingly medicines safely, and at an appropriate ritonavir, against Sars-CoV-2. Funded by useful to laboratory scientists. A dose and frequency, ‘whether that the Bill and Melinda Gates Foundation, partnership announced between be an OTC painkiller, or an antiviral and supporting global collaboration in Elsevier and ExactCure provides a medicine,’ Fabien Astic, ExactCure the drive to develop new treatments for software platform collaboration to co-founder, said. ‘This can help to Covid-19, the centre offers researchers develop and offer to hospitals – without prevent underdosing, overdosing, a workbench of in-silico modelling tools, charge – drug-specific exposure and to prevent drug-drug interactions integrated with existing and emerging models for 20 already approved or adverse events relating to the data. medicines that are being tested as individual’s health status, or even The centre offers an accessible potential treatments for Covid-19. genetic profile. outreach of the expertise that Certara Each drug-specific model, ‘The AI-based software derives the provides in the global Covid-19 generated using ExactCure’s AI-driven personalised guidance according to key Therapeutics Accelerator, which has simulation platform, will help to predict patient-specific characteristics such been set up with an initial $125m in a drug molecule’s pharmacokinetic as weight, age, gender, renal and liver funding from the Gates Foundation, properties in each individual function, smoking status and genetic Wellcome and Mastercard, through www.scientific-computing.com/lig21 5 LABORATORY INFORMATICS GUIDE 2021
“Manual data entry can lead to serious errors, meaning that samples cannot be tested or that the specimens cannot be traced back to the correct source”
which the World Health Organization, simulate drug pharmacokinetics (PK) interaction with the host and symptoms. governments, healthcare providers that can predict and describe how the ‘You can then link those models and industry are collaborating to speed body affects the drug-drug absorption, together and that enables you to the development of therapeutics to distribution, metabolism and excretion simulate what you think might happen treat Covid-19 or prevent Sars-CoV-2 (ADME), and how PK may be altered by in clinical trials. Ultimately, modelling infection. formulation, patient variables such as and simulation can reduce the number Craig Rayner, president, integrated age, gender or genotypic information, of patients, or trial arms required, as drug development at Certara explains: or concomitantly administered well as evaluate the influence of other ‘Certara is providing expertise in medications. design factors on trial outcomes, and translational and clinical pharmacology, The Simcyp Simulator links so improve the probability of success,’ quantitative science and regulatory laboratory data to in vivo ADME data added Nieforth. strategy to support critical stage and when integrated with and extended decisions, clinical trials design and to pharmacodynamic (PD) information Advancing viral testing dosing optimisation for Covid-19. (how the drug effects the body) such With the world’s focus on the pandemic, ‘For a virus like Sars-CoV-2, for as biomarkers or clinical efficacy and LIMS providers are working to develop example, Certara researchers invest safety, is a powerful tool to support solutions tailored to assist in the testing significant efforts in bringing the dosing decision-making in new trials. and management of virus samples. biology and math together to help Keith Nieforth, senior director By streamlining processes, increasing improve decision making for new of Certara’s software division, said: connectivity and reducing manual data therapeutics. One can now evaluate how ‘Designing and running clinical trials for entry samples can be tested more the virus enters cells, how it interacts any drug or vaccine is hugely expensive efficiently and more accurately. and replicates, what the immune system and time consuming, so there is a great Edward Krasovec, director of clinical is doing in response, via sophisticated need to boost efficiency, and improve solutions at LabWare explains: ‘Manual quantitative pharmacology frameworks the likelihood of success. data entry can lead to serious errors, and predictive tools and then simulate ‘The Certara tools can also model meaning that samples cannot be tested new situations,’ he suggested. drug activity at particular sites of or that the specimens cannot be traced ‘We can take huge amounts of action, and look at the physicochemical back to the correct source. When data from preclinical models, in vitro properties of that molecule in the dealing with healthcare, this means testing and clinical experience, as a context of other molecules with potentially very sick patients missing fundamental foundation on which to similar structure and activity, to make out on results from their tests.’ use math engines to model what will predictions on whether the drug will John Gabathuler, director of happen in different trial scenarios, start reach target tissues, such as the lung, if industrial and environmental at to simulate clinical trials accurately, and we consider Sars-CoV-2,’ Nieforth said. LabWare, also highlighted the then add data derived from new trials ‘In the case of Covid-19 importance of removing errors from back into the model, and validate in- drug development, the Certara manual data entry processes. ‘They are silico learning,’ said Rayner. models integrate simulations processes that have not been there Certara’s Simcyp Simulator has been of drug pharmacokinetics and previously. They have had to set these developed as a suite of modules that pharmacodynamics, alongside virus processes up, and therefore they are
6 www.scientific-computing.com/lig21 Dive Into Your Data BSSN™ SciDiver lets you access and analyze your laboratory data with anyone, anywhere, on any device.
Scientific breakthroughs aren’t confined to the bench. Collaborate with remote colleagues and connect your instruments with SciDiver, a secure cloud solution for organizing, harmonizing, and visualizing all your analytical and biological data.
Learn more at bssn-software.com
The life science business of Merck KGaA, Darmstadt, Germany operates as MilliporeSigma in the U.S. and Canada. © 2020 Merck KGaA, Darmstadt, Germany and/or its affiliates. All Rights Reserved. MilliporeSigma, the vibrant M and BSSN Software are trademarks of Merck KGaA, Darmstadt, Germany or its affiliates. All other trademarks are the property of their respective owners. Detailed information on trademarks is available via publicly accessible resources. 34066 11/2020
34066_MSIG_BSSN_SciDiver_Ad.indd 1 11/16/20 8:09 AM LABORATORY INFORMATICS GUIDE 2021
As LIMS providers collect and store data for laboratories, it is crucial they play a role in working with specialised software partners to ensure interoperability. ‘It’s not just about having an instrument that can do the test. That is just one part of the process. If you cannot get that test where it needs to go, to the healthcare provider, patient, or public health authorities, then it is a wasted effort,’ noted Krasovec. ‘Not to mention that the people you are testing are out there, potentially not knowing they are infected, and they continue to infect others. Gabathuler added: ‘That is why we have this enterprise laboratory platform, because there are a lot of parts to it and they can all act up in a nice cohesive going through them for the first time, illness management. In addition to the joined-up way to help in lots of different or they are not as tried and tested, so Covid-19 test, we are also developing areas. You have got a functional the chances of systems not getting a sepsis panel and an antimicrobial- platform and then everything can be the right information can exacerbate resistant panel, and are currently leveraged from that going forward.’ problems. With the current situation you looking for strategic partners for both.’ Rapid adoption of new technologies want to be as accurate as you possibly The firms are aiming to continue requires LIMS providers to be agile in can, as fast as you possibly can, this partnership to include multi-target ensuring interoperability with software because people’s lives depend on it. testing. The combination of Tangen’s partners. This enables them to provide ‘We are trying to help by putting rapid, highly sensitive and point-of-care the infrastructure or platform that can automated software processes in place molecular diagnostics and LabWare’s not only interact with instruments and to help capture the testing data: that real-time data reporting LIMS software laboratory equipment, but also data may be challenging because you are out should enable public health systems analytics or AI software frameworks. in the field,’ added Gabathuler. to react quickly in terms of quarantine ‘There is a rapid adoption of Labware developed the Portable guidelines, patient tracing, hotspot new technologies in the healthcare Disease Surveillance Lab kit in monitoring and infection surveillance. laboratory in terms of a genetic-based partnership with Tangen Biosciences. testing platform which has spawned They recently announced a partnership Maintaining interoperability this order of magnitude difference in for LabWare to distribute Tangen’s Covid-19 demands that laboratories the amount of data that is created – that GeneSpark device as part of the kit in adopt new practices and workflows data has to be managed,’ said Krasovec. response to the pandemic. quickly, but when new technologies ‘Quite often it involves specialised The kit connects to the LabWare are created and deployed quickly technologies to interpret that data.’ LIMS software portal to capture patient interoperability can become a ‘As a LIMS provider, we are not a demographic and clinical information, challenge. As Labware’s Krasovec domain expert in analysing genetic document field collection of respiratory points out, the company’s strategy data. It is important we are able to swabs for Covid-19 testing, attaining has been to recognise that no single get data that may be captured from the sample, and rapidly disseminate this organisation can do it all – collaboration an instrument and interact with data to public health agencies. with the right partners is crucial. the software specialised to do that Beyond Covid-19, Tangen is making With data analytics and AI interpretation of these gigabytes of data a Flu/Covid-19 Panel that can detect Flu applications becoming increasingly that can be generated by sequencing A, Flu B and Covid-19 simultaneously widespread, new data sources and ways processes,’ Krasovec added. ‘That is from one patient sample in a single of analysing data are now available. AI obviously very important, because no processing run, so that patients with flu- and data analytics also asks questions one system is the be all and end all, like symptoms will know whether they of existing data. Has legacy data been and they need to coexist and share have flu or Covid-19, or neither. stored in a way that allows it to be easily information with other systems. Richard Birkmeyer, president and reused in the future? If that is not the ‘We manage the workflow process CEO at Tangen, said: ‘The pandemic is case, then an organisation must clean and there may be data analytics that tragic for many families. Everyone at and order that data before integrating AI goes along with it that could be done Tangen Biosciences has been working into their workflows. by specialised software. Then we are long hours to have our sensitive Interoperability between software responsible for distributing the final Covid-19 assay on the market. More systems, different workflows and the report to whoever it needs to go to. We importantly, we believe the combined various outputs that these processes have a role in the process. It is important Covid-19 and Flu A/B test will be a create, are key to providing a stable that we are able to interact with the n critical surveillance tool for respiratory platform for laboratory data. other systems as well,’ said Krasovec.
8 www.scientific-computing.com/lig21 More time for: exceeding expectations.
Connect your QA/QC workflows to increase productivity & stay ahead of schedule
QA/QC laboratories are all about processes. Processes to manage the lab, processes to manage the data, processes to manage the processes. Thermo Scientific™ SampleManager™ LIMS, LES and SDMS software brings it all together and delivers more for your organization, streamlining workflows, easing compliance and enabling scientists to focus on delivering high quality results, faster.
Find out more at thermofisher.com/samplemanager
For Research Use Only. Not for use in diagnostic procedures. © 2019 Thermo Fisher Scientific Inc. All rights reserved. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. AD80148-EN0219
LABORATORY INFORMATICS GUIDE 2021 Laboratory technology changes
Informatics experts share their views on the future of the laboratory and how things might change due to the added pressure of Covid-19
What do you think will be the biggest a lot of work going on at the moment change in the laboratory? around connected instruments and Richard Milne VP and general how data can flow more easily. manager of digital science at Thermo Fisher: Stephen Hayward, Biovia technical One of the things that 2020 has done marketing manager: is it has created a tipping point in the Transformation of the user experience laboratory. People will find they need with the inclusion of advanced to reconfigure lab space and the techniques. For example, voice configurations of labs. But we are also recognition, where a use case would seeing higher demand to make the lab be dictating observations and results available. utilising scientific awareness in the How can people work from outside recording process. the facility? How can people access Transfer to cloud-based systems, data when they are not inside the driven by corporate IT policy changes laboratory? How can they collaborate – this enables more remote access, when they cannot travel as easily as which is becoming critical in times of a they did? How can they control their pandemic experiments and run their lab without AI – truly leveraging all existing being inside it? knowledge from the lab to better A lot of those drivers that we are guide future work. Finally, augmented seeing in all aspects of society at reality technology which can transform the moment are going to continue to lab process execution – visualising persevere. We are finding that there is additional contextual information, or a very significant increase in people alerts about sample status and pending wanting to see technology shoulder tasks. some of the burden and assist in Many lab technicians are considered the changing parameters of the ‘essential workers’, so they have workspace. We are seeing it in every continued working during a pandemic. industry and every walk of life, but it But the way of working has changed. is also being clearly illustrated in the Teams working in the lab are now split laboratory. into smaller groups that are working We are doing a lot of work around in shifts to minimise contact while cloud-based computing platforms, covering the workload. This makes collaboration environments, data efficient and flexible laboratory moment and data storage. There is scheduling critical.
10 www.scientific-computing.com/lig21
LABORATORY INFORMATICS GUIDE 2021
“We are doing a lot of work around cloud-based computing platforms, collaboration environments, data moment and data storage”
Additionally, all tasks that are not related to physical activities in the lab are now performed remotely. Therefore, it is important to be able to work with experimental data away from the lab while retaining contextual data for decision making, which is typically supported by cloud solutions.
How has Covid-19 changed how the scientific ecosystem works together? Arvind Kothandaraman, general manager diagnostics, PerkinElmer: A major takeaway from Covid-19 has been that every second matters when it comes to a response. In order to be more nimble and agile, labs require tools with high levels of sensitivity and reliability in order to detect disease, develop therapeutics and discover preventive measures that can be taken before there is an opportunity for a surge to begin. Early detection and diagnostics are vital for labs, as screening becomes the new normal. We will also see a shift towards molecular testing and surveillance in general over the next year or two. Covid-19 necessitated this shift, and labs have realised that they must be equipped with life science and diagnostic tools to better manage the spread of infectious diseases now and in the future. While we hope to never experience a pandemic of this magnitude again, it is in our best interest for labs to proactively conduct surveillance to better manage the potential risk. Collaboration among scientists is the backbone of labs. The fight against Covid-19 has been prioritised across the globe, and this has accelerated how all organisations work in a united effort to ultimately serve the public. In that sense, pharmaceutical and biotech, which are conventionally considered competitors, have joined together to work towards the same goal. Information sharing will help www.scientific-computing.com/lig21 11 LABORATORY INFORMATICS GUIDE 2021
ensure the abundance of testing kits distance. The value that our solution “Teams working in and therapeutics for everyone and brings has never been greater in everywhere. The collaboration has today’s world of virtual companies and the lab are now split been unprecedented, and we’ll see distributed research teams. into smaller groups this approach continue in many ways In fact, we have written a white paper moving forward. on the subject of remote data access, that are working in and interested readers can find it on the shifts to minimise Dr Barry Bunin, CEO of Collaborative Scientific Computing World website. Drug Discovery (CDD): contact” While the concept of remote working What are the biggest challenges that is nothing new, the Covid-19 pandemic lab users face? has created a new reality where many Stephen Hayward, Biovia: scientists are forced to spend less Higher project throughput with the still in a less digitised and connected time in the lab and instead work from same number of staff requires efficient state. We expect that this will continue alternate locations. One of the main tools for handling data, observations to increase as the benefits of efficiency, challenges that comes with this is data and result analysis. Distributed labs better innovation, decision making availability – do you have access to means that all data must be available to and faster time-to-market are too your data outside of the lab? How do all team members in real time. compelling. you share data with colleagues and Although most labs have electronic Disconnected systems, rigid collaborate when everyone is physically solutions in place, they are very rarely applications and lack of sufficient separated? And if you do share your integrated and users are forced to support from corporate IT in labs is data, how do you make sure there is transfer data and results manually making it difficult for organisations adequate access control to prevent between systems, which is time- to deploy new technology. Only a unauthorised access? These are consuming and error-prone. Only transformative approach will enable important considerations, in particular flexible, integrated solutions across labs to move to a truly digital lab that in deadline-driven projects where sites and collaborating partners can also allows them to leverage new achieving specific research milestones fulfill such requirements. technologies. This transformative is critical for the success of the No competitive lab can work without approach is typically supported by organisation. digital support for process automation, scientifically-aware collaborative At CDD, we have been enabling data capture, sample management, data business platforms. scientific collaborations for the last 16 sharing and analysis. Most laboratories years through our CDD Vault-hosted in the life sciences space have already Oscar Kox, CEO at iVention: informatics platform. Anyone with implemented digital solutions for We started with cloud from day one and access privilege for a project can compliance and efficiency reasons. we said ‘we want automatic upgrades’ manage and analyse data from any web ‘We are observing that laboratories we do not do custom software. And if browser anywhere in the world, and the in other process industries, as well as we do some custom software it will be whole team can work together in real discrete industries, have started to taken up into the core product, so that time, even when separated by physical implement electronic tools too, but are we can still do the automatic upgrades.
12 www.scientific-computing.com/lig21 Dotmatics for Collaborative Research For more information or to request a demo go to dotmatics.com
The Dotmatics solution for collaborative network research is widely used by global pharmaceutical and biotech companies as well as the world’s leading CROs. Our hosted collaborative platform provides real-time scientific data exchange, informed project management and, when appropriate, shared scientific decision making across the partners to help ensure success whatever the project model.
··· With Dotmatics You Can
Deploy a Cloud Hosted Collaboration Platform Use Realtime Scientific Data Exchange Accessed by all partners, project members can be spun up Molecules, sequences, assays, experiments, scientific and down quickly images, and analytical as well as text and data
Enable Cross-Partner Scientific Workflows Manage Projects and Monitor Performance Capture experiments, molecular and biologics entities, Assign work, track the status of work requests, and monitor samples and assay results. Shared decision support tools progress drive cross-team decision making ··· Streamlining Scientific Workflows The Dotmatics Platform provides a comprehensive scientific informatics solution which can map to all stages of a research workflow.
Capabilities include: • Database management with federated searching ··· • Electronic lab notebook for chemistry, biology, analytical and About Dotmatics formulation • Assay data management Dotmatics is a global organization supporting • Laboratory data automation and management science-driven research around the world. Dotmatics • Entity registration - biology and chemistry offices are situated to allow real-time support at any • Inventory management and work request system time, ensuring your collaborative research can proceed • Visual data analytics at full speed. LABORATORY INFORMATICS GUIDE 2021
We have now developed the automated OQ scripts [IQ/OQ Validation Protocol] and system to enable the automated execution of these scripts. When we release software and you do it agile, every two weeks, it is impossible to have everyone testing the software manually. For other providers, it can take months to upgrade and even longer to complete the validation. We do not want to see upgrades taking longer than days. We will validate, put the OQ scripts in a document and even add some screenshots. The system will try to login in Chrome or Edge and this is how we do it. It generates a complete report. We are still doing really well in implementations because we can work with people using Teams meetings to do configurations together, because we are in the cloud. From an implementation standpoint it is massive, because some people who cannot work right now as “A major takeaway Organisations (CROs) and Contract they cannot go to the office, they can Development and Manufacturing test software, when normally they would from Covid-19 has Organisations (CDMOs) that they are do that next to their day jobs. been that every working with, as well as within their own The second thing is that if you look organisation. at the old-fashioned implementations second matters Our pharma services group is from the more conventional providers, when it comes to a implementing our capabilities to you need a VPN connection and then manage their [customer] CDMO there are still Excel files that are stored response” operations across 25 sites. This has on your PC in the office. This means enabled us to partner with them as a you cannot get to all of your data. The customer ,but also as a part of Thermo old-fashioned implementations with the our digital science team to make sure Fisher to find the ideal state as they talk client on the PC in the office means that that [Amplitude] is working with minimal about their scientific ecosystem, and you cannot access that when you are touch, minimal operator system. how they take it from where they are working from home. today. Trish Meek, director of marketing at What role do automation and Thermo Fisher: Richard Milne, Thermo Fisher: integration technologies play in One of the key things we are seeing We recognise that a lot of organisations overcoming laboratory challenges? when we talk about connectivity and have legacy investments in software Richard Milne, Thermo Fisher: lab automation and ensuring that applications and many of those We are looking increasingly at how you organisations are leveraging their data can be deeply embedded in their can connect devices to look at their effectively, is the value of the scientist. processes. Rather than looking at this operating parameters and confirm that For years people were filling in the as a revolution where you disrupt the they are online and within range. gaps, with a lack of automation the existing situation. We are looking at it We want to be able to do that from scientists would fill the gap and do that more as how do you integrate into that, a mobile phone at a safe distance work. I think there is a recognition from and therefore protect the investments to ensure that your experiments are organisations that the scientists are that people have made in other running, regardless of where you may their greatest asset, and any way that software tools but provide integration be. they can automate and integrate data across those, so people can get an We are doing a lot of work with our and the workflow means that scientists easier customer experience and also laboratory automation team at the can be more effective and focus on the the value of the integration from the moment. One of our most recent, big science itself. different toolsets. and impactful solutions that we released When we talk about integration with I don’t think Covid-19 is causing into the market was the Amplitude our customers, there are a few different it. This is just my perspective, I am solution, which is the high-volume pieces. There are the partnerships basing this on my own conversations Covid-19 testing solution that is being they have between organisations, the with customers, but my feeling is that used across the world at the moment. integration with outsourcing and so we Covid-19 is the catalyst for this change. There is significant integration work with our customers to facilitate the It would have happened anyway, but between our laboratory automation and integration between Contract Research slowly and more sporadically.
14 www.scientific-computing.com/lig21 SDMS
LIMS PORTAL
NEW INSIGHTS, MEANINGFUL MOBILE CONCLUSIONS, BETTER DECISIONS ELN Part of our Integrated Solution, STARLIMS Advanced Analytics allows you to quickly
answer questions for root cause analysis, ANALYTICS CLOUD identify bottlenecks causing performance issues and opportunities for improvement.
Proactively act on facts, apply remediation plans, and see the outcome of your actions, ultimately resulting in a more efficient organisation.
C
M
Y
CM
MY
CY
CMY
K
Discover more about STARLIMS solutions at www.informatics.abbott Request a demo today!
INFORMATICS LABORATORY INFORMATICS GUIDE 2021 Open science drives bioinformatics research
The European Bioinformatics Institute is developing tools and infrastructure to promote open science and provide programmatic access to biological data
oday the European Bioinformatics Institute T (EBI) maintains the world’s most comprehensive range of freely available and up-to-date molecular data resources. It provides 307 petabytes of raw data storage for bioinformatics data and receives more than 62 million web requests per day. The focus on open science and delivering infrastructure to support scientists’ access to scientific data is at the heart of EBI’s mission to support bioinformatics research. The first steps to creating bioinformatics data resources so that scientists and researchers could share sequence data in Europe were in 1980, with the creation of the EMBL Nucleotide Sequence Data Library (now EMBL Bank, part of the European Nucleotide Archive). The archive was established and scientists realised other resources of bioinformatics data; providing in 1980 at European Molecular Biology were being created that would also be training on the use of these resources; Laboratory (EMBL) in Heidelberg, of great value if they could be shared hosting the Elixir hub; and supporting Germany. with the wider community. What began scientific services and resources such Johanna McEntyre associate as a straightforward task of abstracting as the European Nucleotide Archive director of EMBL-EBI services, senior information from scientific literature (previously the EMBL Data Library). scientist and head of literature soon grew to a major database, with services, said: ‘EBI was started more researchers submitting data directly. Open access infrastructure supports than 25 years ago now with a remit In 1992, EMBL Council voted Covid-19 research to provide data resources for life to establish the EMBL-European Another aspect related to this open sciences. The original resource, the Bioinformatics Institute (EMBL-EBI) and access data is research paper EMBL data library, housed nucleotide locate it on the Wellcome Trust Genome preprints, which have been very sequences for research. Sequencing Campus in Hinxton, UK, where it would valuable for sharing data during technologies were taking off. They had be in close proximity to the Wellcome the pandemic. A preprint allows moved out of being a research project Sanger Institute. In September 1994, researchers to share results with the in themselves, to something that more EMBL-EBI was established in the UK. scientific community in advance of and more people were doing. ‘EBI was created almost 27 years peer review, making data available ‘There was a requirement for ago. The institute grew from just a few much faster than was previously a database to keep these things, pioneers at that time to an 800-strong possible. because there is a lot of value in institute today,’ noted McEntyre. ‘Another very recent thing that comparing sequences from different EBI’s mission is split into five we have done is a project based on organisms.’ distinct areas: computational Covid-19 preprints,’ said McEntyre. This initial EMBL data library grew research; supporting industry use ‘Instead of being behind closed doors
16 www.scientific-computing.com/lig21 SCHEDULE A FREE DEMO AShare FREE your plansDEMO with Share your plans with Open science drives [email protected] We [email protected] ready to take up We are ready to take up your challenge! bioinformatics your challenge! research
MORE THAN LIMS WITH LES
iLES enables efficient automation and regulatory compliance iLES enables efficient automation and regulatory compliance for your R&D-, Quality and Production processes with the for your R&D-, Quality and Production processes with the state-of-the-art iVention Lab Execution Platform. state-of-the-art iVention Lab Execution Platform.
A FRESH APPROACH IN LAB AUTOMATION Enable• Single efficient All-in-One Platformautomation and• regulatory Easy to implement compliance Enable• Single efficient All-in-One Platformautomation and• regulatory Easy to implement compliance for• 100% your web R&D-, based Quality- and Production• Continuous processes Delivery with the state-of-the-art• 100% web based iVention Lab Execution• Continuous Platform. Delivery •state-of-the-art Cloud computing iVention Lab Execution• Free (automated)Platform. Upgrades • Cloud computing • Free (automated) Upgrades • Mobile First • Low Total Cost of Ownership • Mobile First • Low Total Cost of Ownership
GLOBAL HEADQUARTERS +31GLOBAL (0)38 HEADQUARTERS452 83 75 / [email protected] Zwolle,+31 (0)38 The 452 Netherlands 83 75 / [email protected] Zwolle, The Netherlands REGIONAL OFFICE US +1REGIONAL 502 909 0317OFFICE / [email protected] US Louisville,+1 502 909 USA 0317 / [email protected] Louisville, USA REGIONAL OFFICE APAC +91REGIONAL 79 40067697 OFFICE / [email protected] APAC Ahmedabad,+91 79 40067697 India / [email protected] Ahmedabad, India
[email protected] / +31 38 452 83 75 [email protected] / +31 38 452 83 75 ivention.nl
Adv-iVention2020.indd 5 12-11-2020 08:26 Adv-iVention2020.indd 5 12-11-2020 08:26 LABORATORY INFORMATICS GUIDE 2021
“Open science is a great equaliser”
science, as more people can see the outputs and access the contextual data that supports the research paper. However, linking the data is also very important for research, and trust in that research. ‘Coming from the data point of view, you might argue that linking to the data is less important, but where that really comes into its own is where people you just post your finished manuscript Europe, and so it is called Europe PMC,’ have developed algorithms to search to a preprint server. When you do that, said McEntyre. through the data,’ stressed McEntyre. what happens is a very light screening Europe PMC is a global, free, ‘I think, and many other people think, process. That means that your results biomedical literature repository, that linking to the data is very important, are available in 48 hours of submitting providing access to worldwide because you need to have as big a it, as opposed to months. life sciences articles, preprints, collection as possible of open access ‘During the pandemic pre-prints micropublications, books, patents literature for people to invent new ways have been very important in very and clinical guidelines. The resource of doing things. For example searching quickly sharing results. The model is currently contains more than 36 million or browsing literature.’ that it doesn’t avoid peer review, it’s abstracts and more than five million full- In order for AI and machine learning just that peer review happens after the text articles. A subset of the full-text to be possible, data needs to be made fact,’ McEntyre added. information corpus is the open access available, and in a way that allows literature that can be downloaded and scientists to generate huge datasets. Need for open access research data used from the FTP site, for example for Creating a large database of open data Today EBI has a huge collection of tools text-mining research. enables researches to access data and data resources, including Europe ‘This database was originally created from several different sources that have PMC, a full-text database of research to support those open access policies all been stored and made available for articles and abstracts that are openly introduced by research funders, but reuse. available for everyone to read, with a it does lots of other things as well. If data is not managed in the correct subset of those available for reuse. One of the most important things is to way, these types of activities are made ‘The point of running this database provide bulk downloads and APIs for much harder, as individuals would is because funders of life science programmatic access to the content,’ need to seek out that data manually research in the UK needed some said McEntyre. from several different sources. This infrastructure to support their open- ‘The second very important data may be stored using different access policies. Very simplistically thing is linking to the data. When formats, making data cleansing and put, their policies will say something someone deposits data into one of pre-processing necessary. ‘Managing along the lines of “we expect all our our databases, it is usually because in the correct way means open data, it researchers to publish the outcomes of they have generated the data in the also means storing in formats that can their research openly”,’ said McEntyre. course of doing some experiments, readily be consumed by machines and ‘That will often specify that these and typically those experiments will humans, and having the appropriate papers should have a CC-BY licence, be written up in the form of a research amount of metadata,’ said McEntyre. a licence that allows people to reuse paper. You want to link the data to the Open science infrastructure can that work without having to request literature for the biological context, and open up new ways of conducting permission – this can be very important you want to link from the paper to the research and interrogating data, but for machine learning and AI,’ data, to show the provenance of the ultimately the driving factor of open As the data volumes and types research results,’ McEntyre said. access research is to drive scientific of resources increased, some of the ‘This means that you can look at discovery by sharing insights with other organisations funding research were the data behind the paper and see researchers. trying to find a way to make results for yourself whether it supports the ‘Open science is a great equaliser. openly available. ‘A lot of research assertions that have been made in the It is far more likely that someone in a funders, not just EBI, needed a research paper. That linking between developing country is going to have an repository to support that open access the literature and the data is very internet connection, than access to a policy. They invented what was called important in both directions.’ library of scientific data. UK PMC at the time, which has also now Open access to the data generally ‘It opens up research to everybody in n grown to include 30 funders across improves the reproducibility of the the world,’ said McEntyre.
18 www.scientific-computing.com/lig21 ACD/Spectrus Because Analytical Data is at the heart of R&D
Learn more: www.acdlabs.com/Spectrus
Realising the potential of data emil Europa Market through accurate research, Intelligence Limited lead generation and client-led community creation
Scope fresh markets
Bespoke lead generation
Niche marketing
Make your data work harder
Research industry events
GDPR ready?
Europa Market Intelligence Ltd Tel: +44 (0) 1354 610188 [email protected] www.europamarketintelligence.com small. smart. Think Think LABORATORY INFORMATICS GUIDE 2021 The leading-edge of genomics research
Wellcome Sanger Institute’s Julia Wilson tells Robert Roe about the research centre’s role and impact on the wider scientific community
he Wellcome Sanger Institute goals at Sanger which adapt and “When the rest aims to tackle some of the evolve over time to constantly T most difficult challenges in push the boundaries of scientists’ of the world can genomic research. This demands understanding of genomics. do what we do, science at scale alongside a ‘The history, in a nutshell, was that creative approach to research that Sanger was established to sequence then we need to pushes the boundaries of scientific that first human genome. That took change direction – understanding. ten years and cost millions of pounds Sanger’s scientific niche is in to get that one first human genome we should always large-scale, high-throughput biology, sequenced,’ said Wilson. ‘We needed be breaking new often incorporating systematic to then be able to understand the genome-wide screens. These are information in the human genome, ground” enabled by major data generation map it to health and disease, so platforms in DNA sequencing, and scientists can compare between genetics with an accompanying large populations. Pushing the boundaries IT platform supporting computational ‘Since then, Sanger has been One of the mandates or hallmarks data analysis. studying the biology of genomes of scientific research at Sanger is An overarching theme of the – the DNA code. Everything we do the constraint drive to break new centre’s science is genome variation; at the Sanger Institute involves ground. Pushing the boundaries of naturally occurring and engineered, understanding genome sequences understanding in genomics requires inherited and somatic; explored in and applying them to improve human that the focus must frequently shift, as human beings, pathogenic micro- health or increase the understanding the understanding of a certain topic organisms, human cells and mice. of the living world,’ added Wilson. ‘Our becomes more ubiquitous. The Wellcome Sanger Institute mission is to advance understanding ‘When the rest of the world can do Associate director Julia Wilson of biology and to improve health. what we do, then we need to change describes the history of the institute, Everything we do is about genomics direction – we should always be which highlights the research so that runs through all of our science.’ breaking new ground in genomics,’
20 www.scientific-computing.com/lig21 LABORATORY INFORMATICS GUIDE 2021
said Wilson. ‘That means we are at “There is always that push to adapt the leading edge of technologies but also thinking about where genomics and evolve. Take on some of the can take us. In that sense, it is quite a biggest scientific challenges” The leading-edge of fundamental research organisation.’ The current research programmes at Sanger are split into five distinct fields; cancer, ageing and somatic mutation, programme has evolved, because to the DNA pipelines. Some of these are genomics research cellular genetics, human genetics, remain at the leading edge we have had trained at PhD level and beyond but they parasites and microbes and the Tree of to pivot and change direction. There are driven by working in team science Life. have been many examples of this over to deliver something that is greater than All of these projects are research at the organisations history. the sum of the parts,’ added Wilson. scale, producing vast amounts of data ‘We get funded in five year tranches, which must be analysed. ‘We have got so we can take on projects that may last Open science an enormous fleet of data generation – five years, ten years or beyond. We can Another hallmark of Sanger science is particularly DNA sequencing machines take on those riskier projects,’ added that the tools, software, data and other that generate vast amounts of data Wilson. ‘There is always that push to resources at Sanger are made freely that needs to be interrogated and adapt and evolve and take on some of available to the scientific community. interpreted to generate findings,’ added the biggest scientific challenges. It is This means that other organisations Wilson. a mixture of the technology and the can pick up these resources and carry Two of the largest projects being ambition and evolution to remain right on the work, taking it in interesting run are the Human Cell Atlas (HCA) at the cutting edge.’ directions as Sanger shifts focus. and the Tree of Life. The Cellular However these large-scale projects ‘Everything we produce is made Genetics’ Programme jointly leads do not come without their own freely available to the scientific the HCA global consortium alongside challenges. For Sanger this can mean community with the expectation that we the Broad Institute. The HCA vision is want others to take that data and those to create comprehensive reference tools and build on our discoveries. We maps of all human cells – the 37 trillion cannot follow all of the leads from the fundamental units of life – as a basis data that we generate, so we want that for understanding human health and data to be used by others,’ said Wilson. diagnosing, monitoring and treating She also noted that this focus on disease. open science was adopted at the start The Tree of Life investigates the of the Sanger Institute. ‘This happened diversity of complex organisms at the very outset, when genomics was (eukaryotes) through sequencing a new thing and our founding director and cellular technologies. Sanger John Sulston was working on that first generates and uses high-quality genome at the time. It was mandated genome sequences to explore the this data should be released in real-time evolution of life, provide the raw for humanity to benefit,’ added Wilson. materials for new biotechnology and ‘International parties who Julia Wilson deliver tools and understanding for contributed to that first genome signed biodiversity conservation. This project up to these principles and historically aims to sequence approximately 66,000 working to develop new methods or it used to be released each day. There Eukaryotic organisms. tools that can support genomics at an was a ticker tape above reception and However while these ‘juggernaut’ unprecedented scale. the genomic data would go across as it projects may take five to ten years to ‘Another hallmark of Sanger would come off the machine. Obviously complete, ‘the programmes adapt and science is that because we are a we cannot do that any more because change to find new challenges and core-funded institute, we invest in this the data has increased by so much, but break new ground in genomics. Some vast scientific infrastructure. We have genomics was founded on open data. have evolved. The cancer programme got one of the largest fleets of DNA Wilson stressed that this drive for was previously focused purely on sequencing machines, definitely the open data is necessary in genomics looking at genes associated with largest in Europe but one of the largest research, because a single genome is cancer,’ said Wilson concentrations of that technology in of very little use. ‘If they are all locked up ‘Now everybody can do that and as the world. We have to be applying it in individual labs, then none can benefit it has been implemented into genomic to projects that only we can do – like from this,’ Wilson said. medicine, we no longer need to make sequencing all of life in the UK, or ‘It is a principle of Wellcome funding the associations between genes and looking at 37 trillion cells in the human as well. Wellcome, as a funder, has been cancer. The programme evolved to look body,’ said Wilson. so influential, and that ethos of open at the ageing process and the links ‘A huge amount of our budget goes science has filtered through Sanger n between cancer and ageing, and to take on kit and consumables, but also teams since it has been open,’ Wilson said. a deeper dive at what we call mutational of real deep-domain technical experts signatures. that run these pipelines. We have got Julia Wilson is associate director at Wellcome ‘That is an example of where the expert, skilled technical staff running Sanger Institute
www.scientific-computing.com/lig21 21 LABORATORY INFORMATICS GUIDE 2021 Digital drive laboratory transformation
Sophia Ktori considers how software can transform the laboratory
hoosing a system go into labs, see how they operate, and efficiency. Not infrequently, that offers flexible and try to understand their end-to- implementation of a new platform ‘Cconfiguration to match end processes. We need to see what might also highlight processes that specific teams’ needs is key to digital they are struggling with – they may be may have been partially buried. ‘We’ve transformation,’ says Sharon Williams, still relying on spreadsheets that get had customers come to us and say Interactive Software’s product emailed between people with little or no that they need to establish an SOP for director. The UK-based firm works with security, for example – and then we can a process that they only realised they universities and pharma to configure highlight those deficits.’ were carrying out when they automated its Achiever Medical LIMS, designed It’s ‘gap analysis,’ at a high level, the workflow,’ said Williams. for managing complex workflows. she continued, which is more than Understand the ultimate endgame It’s important to look at the just trying to reduce or remove the and you can work backwards from operational requirements of any need for manual data input. ‘Once there, suggests Williams. ‘People potential user, and to understand what we understand where they are now, tend to get tied up with looking at the they already have in place to manage and what their aims are, we can software platforms that are on the their workflows, and where, or what then demonstrate how we can fill market, rather than starting with what their deficits are, Williams noted. ‘We the gaps and build in value, security they want to achieve and how they
22 www.scientific-computing.com/lig21 LABORATORY INFORMATICS GUIDE 2021 want to get there. Realistically we can’t “It will always be change the world in one go. Our aim is to try to break the problem down more difficult to and look at what is going to have the implement for the greatest impact. Then we can start from there and work outwards.’ R&D Labs, just
Is a LIMS always necessary? because the work Organisations may also try to that’s being done shoehorn their existing processes into mismatched legacy software, either is typically less through configuration, customisation routine” or upgrades. ‘This may seem like the logical option, but if the software isn’t designed to do the job, then the outcome may be disappointing, and EMEA, at Abbott Informatics, feels it costly,’ Williams stated. is not uncommon for organisations ‘You have to be realistic about what to be reliant on paper and/or Excel, your existing software can do, and especially when it comes to performing automatically generate a PO to order acknowledge when it may be better lab procedures, for example, sample new inventory, once a threshold level all round to look for something that is preparation. has been reached,’ added Schüler. more fit for that purpose.’ ‘We see that even in 2020 there In fact, companies are quick are still companies that haven’t yet Consider user acceptance to assume that they will need an implemented fundamental IT software ‘For any organisation considering expensive, complex LIMS platform solutions, such as an enterprise advanced technologies, the human whereas it’s not always a given that a resource planning (ERP) platform.’ element is a major consideration,’ LIMS will be necessary, she continued. For these organisations, in particular, Schüler continued. If we think about ‘If you are only dealing with a couple but also for those that might be much implementing relatively well-known of hundred samples and there is no further down the digital road, it is critical digital systems, whether that be complexity associated with the data to be realistic about immediate goals. barcode scanning, or transitioning associated with those samples, or A good starting point, according to from other paper-based workflows to what you are doing with them, then Andreas Schüler, technical solution tablet-based systems, it’s likely that the commercial sample tracking software design manager EMEA at Abbott end-user will only have to learn how to may be sufficient to help you manage Informatics, could be looking for use a new touchscreen digital interface samples. They are reasonably priced, opportunities to implement software for data recording and access. ‘For this and would do the job for you.’ that will offer quick and immediate type of digital system, the threshold Interactive Software works with benefits. for user acceptance probably isn’t that those organisations that do have the ‘For example, using mobile great,’ Schüler suggested. ‘Plus, users scale or complexity of workflow to technologies and associated software can see the immediate benefits of not require an informatics infrastructure for functions – such as environmental having to record their data manually, founded on a LIMS for sample sampling or sample preparation for scan it into a system, and then archive management. For organisations testing – where there is no ready access that paper original. Instead, they working in areas that involve to a PC, can have immediate time and immediately have their data digitally accessing patient data and samples, error-saving benefits.’ stored and easily accessible. the implications for security, and The ubiquitous nature of barcoding ‘Progress to the concept of using permissions for individual users, are has now made this a relatively simple more complex technologies, whether uppermost, and so the concept of form of digitalisation to implement, that be sophisticated voice control, digital transformation may be highly suggested Schüler. ‘It won’t or augmented reality, and there may reliant on security,’ she noted. The necessitate high overheads, and the well be more human resistance, both ability to set authorisations and access relevant software and equipment – with respect to learning how to use permissions at the individual user level everyone these days is familiar with a the technology itself, but also with the is therefore critical. touchscreen-enabled tablet, or mobile potential that such systems may watch, – is easily integrated into daily working listen, record and report on their every Journey from any starting point practices.’ move throughout the day.’ Of course, every laboratory or lab- RFID tagging technology also offers In this environment, end-to-end based organisation will have its own an opportunity to completely automate automation is just more complicated, vision for short- and long-term digital inventory. ‘Stock management can Schüler noted. ‘It will always be more transformation, according to where become a self-documenting process, difficult to implement for the R&D Labs, they already are on their digital journey. with the benefit that you always are just because the work that’s being Some organisation’s labs and aware of where any given piece of done is typically less routine. The more businesses have taken steps to inventory is, and how much of any routine your work is, the easier it is to become paperless, but, Gabi Koberg, inventory you still have. Not only optimise and make it more efficient senior regional sales manager, that, but feasibly the system will digitally.’ www.scientific-computing.com/lig21 23 LABORATORY INFORMATICS GUIDE 2021
“It’s more feasible to layer on things such as machine learning, because you have laid the foundations of really robust, rich datasets, which have incredibly detailed metadata”
Digitisation and automation is a key goal also for the R&D lab, Koberg continued. ‘Implementing advanced technologies, such as predictive modelling, could allow labs to reduce the number of experiments they are carrying out, and save on both resources and time. Such technologies can feasibly aid in the design of experiments that provide more insight, which would reduce development time, and ultimately speed time-to-market for new products.’ Speeding drug development can close the gaps in digitisation and The ability to reuse data is really Ultimately, digitisation in the pharma automation gaps in the R&D cycle. ‘This important for maximising insight from or biotech lab will help to speed the cycle typically starts with a hypothesis historical experiments. ‘One key priority identification of new targets and the or question, against which an is to reduce the amount of unstructured development of drugs, vaccines or gene experiment is designed,’ he explained. data, and so put as much data and therapies, suggested Markus Gershater, ‘The experiment is then executed, the metadata as possible into a structured co-founder and CSO at UK-based resulting data is collated, recorded format that can be easily accessed and Synthace. Embracing smart software and reported, and data analysis can mined in the future,’ added Koberg. that can automate the complexity then be carried out. That analysis associated with experimental design subsequently informs the design of the Data standards and execution will take the benefits next experiment.’ Thinking about data utility naturally of digitisation in the lab beyond There has been a lot of focus leads to the concept of data standards. automating how (and what) data can on automating how results data Schüler said: ‘You want to make sure be directly obtained from analytical are handled, managed and in what that the data you are capturing will still instrumentation, and its management formats, with a view to maximising be accessible for data mining long after and analysis. value from that data, which will then aid the system that created it has been Synthace is developing a new in its analysis to help make next-step retired. generation of software tools that will decisions, he explained. One focus of product development effectively speed up how scientists However, the design, planning and at Abbott Informatics is to enable labs can design and carry out experiments execution of those experiments is still to progress their digital transformation that will help to answer highly complex very much a human process. ‘Scientists and enable that end-goal of a seamless, biological questions. By doing this it today will commonly use tools such end-to-end automation and digital should be possible to maximise the as Excel to help them work out their data handling, Koberg noted. The firm depth and utility of data that can be experimental plans,’ and electronic lab maintains that its StarLIMS integrated derived from those experiments, and notebooks (ELNs) are used to record solution has long been at the forefront the associated metadata that can their processes, SOPs and results, of LIMS-based platforms that are map every step of the experimental Gershater said. ‘These tools are digital designed to facilitate interfacing and execution. ‘It’s a concept of digital aids to design,’ but they don’t automate integration of typical laboratory and augmentation that we call ‘computer- the detailed experimental planning. other enterprise hardware and software aided biology,’ Gershater noted. In reality, planning experiments platforms. The aim is to harness software that is a hugely complicated task, he
24 www.scientific-computing.com/lig21 LABORATORY INFORMATICS GUIDE 2021
Taking the limits of help its own labs execute the type experimental design of science that otherwise wouldn’t The vision for the future is to enable have been possible. ‘We realised that scientists to design and run whatever the platform would have much more experiments are required to address impact if we pushed it out across all of biological complexity, without these biology, instead of keeping it in house,’ human limits, he continued. Without Gershater explained. such constraints, scientists should be The firm started marketing the able to generate more sophisticated first iteration of the Antha software datasets, because the design of the in 2017, and the most recent version experiment has been set up to optimise can interface with most state-of- the value of each run, and automation the-art laboratory robotic systems. can carry out these complex designs. ‘Importantly, we have our own ‘If you then are able to generate laboratories,’ Gershater noted, and so datasets that are very well structured the platform continues to be developed for addressing the hypotheses that through experience with real-world you just looked to address, you can experimental scenarios and setups. have very sophisticated analysis on the The firm has close working top of those sophisticated datasets. relationships with its clients, which And that’s when it will be more feasible include major pharma and biotech to layer on things such as machine companies – such as Merck & Co in learning, because you have laid the the US, and Oxford BioMedica in the foundations of really robust, rich UK – and with some of the major liquid datasets, which have incredibly detailed handling robotics and other hardware metadata. This depth of metadata providers. Synthace also continues completes that experimental map, to close research links with Microsoft maximise context, which provides the Research. foundation for then building machine learning on top,’ stated Gershater. Completing the circle Synthace’s flagship cloud-hosted Synthace clients are demonstrating platform Antha allows scientists to the utility of the Antha platform to plan complex experimental protocols, improve how complex lab experiments suggested. ‘Powerful experimentation execute the workflows – through are designed, set up and executed, is a requirement for trying to address direct interface with liquid handling Gershater noted. ‘Oxford BioMedica, biological complexity, but it can also be robotics – and then associate and for example, has really embraced the very difficult to carry out by hand. Each integrate resulting data and every point concept of digitising that complete experiment can take a huge amount of of metadata back to the experimental experimental loop, and is using our very meticulous planning, and running source. platform for execution, and for collation experiments may involve 14-hour days ‘Our software maps out exactly of data, and are collaborating with of complex manual pipetting steps. what has to be done to fulfil a particular Microsoft Research to add artificial ‘So, if experiments are limited at the experimental design,’ Gershater said. ‘It intelligence on top of that collated data, planning or execution stage, it doesn’t works out every single liquid handling in order to loop back round again to matter how much of the rest of the lab action that’s needed, and then drives experimental design.’ is digitised, there will always be limits in the robot to carry out the experimental Ultimately the aim is to enable a terms of experimental feasibility.’ steps as defined. So that means completely interconnected digital you know exactly what’s happened laboratory ecosystem, and while throughout the entire experiment.’ In Synthace is currently working with effect, the software generates a kind clients on specific applications, the of ‘experiment digital twin,’ which is aim is to roll out comprehensive digital “Antha can be then executed in the lab, he suggested. solutions for broader applications. ‘Integrate this capability with complex Citing Oxford BioMedica as an interfaced with data handling and management, and example, Gershater explained how the ELNs, LIMS and you get much closer to the vision of Synthace software can have a tangible seamless digitisation. With this as an impact on the value of experiments. other emerging ultimate goal, Antha can be interfaced ‘What’s really encouraging is when digital tools with ELNs, LIMS and other emerging you see signs that scientists are using digital tools to generate a potentially our tool to do the kind of science that to generate a gapless end-to-end workflow.’ they otherwise just wouldn’t be able to potentially gapless Having started life as a biology consider. Computer-aided biology is company focused on addressing how people could work in the future, and end-to-end biological complexity in process represents an ecosystem of different development, Synthace initially tools we think will be required for truly workflow” n developed the Antha software to digitised lab working.’ www.scientific-computing.com/lig21 25 SPONSORED CONTENT
for entities and see full details about Do you need a chemical the structures, including information on and biological stereochemistry or similar sequences. Compliance – labs need to comply registration system? with government regulations. A good registration system can help ensure there are no surprises at egistration systems can be systems are a step up from some lab inspections or audits. Since the useful IT tools in the arsenal chemical databases, which simply store information is in a single, central R of labs that are looking to the molecule without some of the more location, reports can be made quickly, streamline their workflows. As the name fine details about stereochemistry or accounting for all present entities. suggests, these software systems are associated protocol data. designed to help track the different Biological registration offers Comparison with LIMS and ELN chemical or biological entities used for functionality that lets users define, Laboratory Informatics Management experiments, as well as ones created in register, query, and report on biological System (LIMS) and Electronic the lab as intellectual property. entities including proteins, enzymes, Laboratory Notebook (ELN) are related A core function of registration antibodies, DNA, RNA, cell lines, laboratory informatics tools that can systems is the ability to generate plasmids, proteins, siRNAs, and protein- have overlapping functionalities with (or mirror) unique identifiers that drug conjugates. It also includes tools registration systems. While LIMS unambiguously identifies each entity for managing relationships between typically follow pre-defined generalised and batch combination. Among other biological entities, collecting details workflows defined at the level of lab functionality, these systems support on individual entities such as protein management, ELNs tend to be more the ability to capture information on expression information, and generating personalised and flexible to change by complex chemical and biological chemical representations of entities individual researchers. molecules, including details about where possible. This distinction makes sense in the their structure, various physical and context of regulated environments, chemical properties, and assay testing Benefits of registration systems where LIMS are needed to support data. Findability – perhaps the most the tightly regimented workflows Broadly speaking, entities that can important reason for registering entities and structured data required in these be registered fall into two categories: is also the most obvious, findability. spaces. With their more fluid nature, 1. chemical molecules Being able to find what’s needed for ELNs may be better suited for research 2. biological entities a given test at any point saves time, and discovery environments, where Some registration systems and results in less frustration for changing workflows and unstructured specialise in handling one category, researchers. Labs can have hundreds data are more of the norm. while others, such as CDD Vault by or thousands of molecules and/or In contrast, registration systems Collaborative Drug Discovery, are biologicals in stock at any time. These are more similar to LIMS in their designed to accommodate both. include reagents, as well as entities structuredness, but focus more on Chemical Registration includes made for testing as the core part of organising structures and activities tools for entering individual compounds an organisation’s intellectual property at the chemical/biological entity level, and groups of compounds, searching portfolio. rather than the sample level. for compounds by structure, and for However, the lines between all assigning unique identifiers for each Uniqueness – a related and equally these systems are increasingly compound that comes into the lab. important consideration, for labs fluid. For example, CDD Vault offers These systems include functionality for that work with chemical compounds fully integrated registration system establishing and showing relationships or biologicals, is being able to track and ELN, as well as entity-tracking between individual compounds and important details about an entity features typically expected of LIMS. families of compounds, and for linking (lots, salts, etc) that are related to When evaluating various solutions, compounds to associated screening uniqueness and a cause for ambiguity researchers should look beyond the data in the lab. Moreover, registration or duplication errors. Registration name to find a system that matches the systems can flag when researchers needs of a particular lab. are unwittingly duplicating entries or Across industries, chemical and “These systems screening different forms of the same biological registration systems add support the entity. These systems can distinguish significant value to R&D teams working between entities with similar structures, with large numbers of chemical and ability to capture sub-structures or sequences. biological entities and associated data. information on Implementing CDD Vault as part of a Tracking – another reason to register larger suite of research informatics complex chemical your entities using a registration tools can improve your operational and biological system is their ability to store chemical efficiency, reduce risks of human error, and biological entities for future save time and ensure the integrity and n molecules” tracking. Researchers can run queries legacy of your work.
26 www.scientific-computing.com/lig21 The science of appliance Discover Scientific Computing World Online
l Read news as it is published l See industry press releases l Refer to archived feature content l View webcasts l Study white papers l Find relevant suppliers for your business l Subscribe to the magazine, find our Twitter feed, or connect to us on LinkedIn
SCIENTIFIC COMPUTING www.scientific-computing.com WORLD LABORATORY INFORMATICS GUIDE 2021 Looking at cancer
Robert Roe discovers from Dan Ruderman, assistant professor of research medicine at the Ellison Institute USC, how advances in computer vision and AI computing are helping pathologists identify cancers more accurately – leading to better treatments
“They are still 0 years on pathologists a pathologist examine specimens has still rely on their eyes an H&E stain done to find out what looking at them ‘8to diagnose,’ says Dan the diagnosis of this patient is,’ said with their eyes Ruderman, who together with his Ruderman. ‘This means that it costs colleagues at the Ellison Institute have zero dollars, because the test has and making those been using large-scale AI simulations, already been done. decisions run in partnership with Oracle, using ‘What is surprising about that is the Oracle Cloud Infrastructure. given the amazing advances we have given the amazing ‘Pathologists use their eyes to had in computer vision for things like advances we have make these decisions so whether self-driving cars and certain modalities they have gone from a microscope in medical imaging, we are not using the had in computer to now looking at digital images that advanced capabilities of computers to vision” have been scanned in from slides, help in these diagnoses to make better they are still looking at them with their decisions for patient care.’ eyes and making those decisions,’ is an important step in the effective Ruderman said. Using computers to assist in treatment of cancer, because it means Their research uses pre-existing diagnosis that patients can potentially receive the Hematoxylin and eosin stains (H&E Today the fields of visual pathology correct treatment faster and without stains) to identify cancer subtypes by and AI and machine learning are having unwanted side effects from training neural networks. being employed to solve particularly drugs that may be ineffective. ‘Every patient around the world challenging questions in the ‘The big question in clinical care who goes through surgery and has diagnosis of cancer subtypes. This is who is going to respond to which
28 www.scientific-computing.com/lig21 LABORATORY INFORMATICS GUIDE 2021 therapy. Once a diagnosis has been “What is common to all of these made, what subtype of, in my case cancer, is it, which determines the therapies, is that patients are going therapies a patient gets.’ to have to suffer side effects but not There are several existing molecular markers that can help identify potential achieve any benefit” treatments but while ‘they are good, they are not good enough,’ argues Ruderman. ‘For example, if there is a and fingerprint technologies have alphabet soup of these kinds of mutation in a patient’s melanoma to meant that the accuracy of prediction mutations or tests you can do to the BRAF gene, they would be given using the H&E stain has risen subclassify these cancer-specific Zelburaf to treat them. But despite dramatically. AUC in the later tests was mutations according to what therapies having this molecular marker, only found to be 0.89, which provides a they will respond to. If you look at the around half of those patients are much better standard for diagnosis. publications in digital pathology people going to respond to that drug,’ added Running on the Oracle Cloud are working on lung cancer, bowel Ruderman. ‘What is common to all Infrastructure, researchers at the cancer, prostate cancer and others,’ of these is that patients are going to Ellison Institute are using bare-metal said Ruderman. have to suffer the side effects of these GPU instances to run and train deep ‘They are not exactly asking the therapies but not achieve any benefit. convolutional neural networks. They are same questions that we are asking but The question that researchers at also making use of Oracle Autonomous people are now digitising those samples the Ellison Institute began to ask was: Database to store a lot of their training and running deep convolutional neural ‘can AI help to make better decisions in and inference data. ‘We have tens of networks on them.’ these cases to predict, not just which millions of rows in these database In this new age of AI and deep patients have these markers, but which tables. Then on the shared file system, learning, Ruderman stressed that patients will respond?’ we have the whole slide images. there is no magic bullet to develop the The initial research looked at Terabytes of data from all of these perfect model. ‘We are still in the age hormone receptor-positive breast slides that have data captured,’ said where it is know-how, trial and error cancer. Traditionally this is done Ruderman. and an art form. The more computing with a $300 immunohistochemistry The hope is to take multiple slides power you have the more room you test, if a sample is found to be and produce a 3D model which could have to experiment and try different estrogen receptor-positive (ER+) then provide much greater accuracy, as architectures simultaneously’ said approximately 60 per cent of patients the amount of data contained in Ruderman. respond to endocrine therapy such as each patient sample would increase This is a key part of the collaboration Tamoxifen. dramatically. between the Ellison Institute and Oracle, ‘Fundamentally these two cancers as the computing power provided by the look the same under the microscope. Looking to the future latter allows researchers to try different If you ask a pathologist to designate Ruderman also hopes that the work model parameters to explore the ways just by eye from this kind of scan – is it done here and at other research that the model can be improved. an ER+ or ER- tumour? They generally centres looking at different cancer ‘People are now getting things to would not be able to do it,’ said types or other diagnoses can help work at a certain level and they publish Ruderman. ‘There are certain subtypes, to develop the frameworks for wider their architecture. You might look at the such as lobular cancers, where the research into this combination of number of layers and try to emulate it cells all arrange in lines which could be medicine, AI and computer vision. ,or build from that existing process or identified as ER+ cancer, but that is a ‘We can take that exact same slide protocol developed previously. fairly rare subtype. that has already been created and ‘That is where having a lot of ‘Can we use AI and all the wonderful extract more information out of it. This computing resources, that we have with advances in computer vision to “read information can tell a clinician that they our collaboration with Oracle, is really the tea leaves” and find things that are may benefit from hormonal therapy. helpful, because it allows us to explore too subtle for our eyes to discern?’ That is valuable because those pills are these things. The short answer is, there The slides are digitised and then cheap, for example,’ said Ruderman. ‘It is no formula, go out for yourself and try broken down into different measurable is information already held in the slides stuff,’ said Ruderman. variables, such as the size of nuclei, they have in their hands. You just need ‘You take something that works, orientation etc which is fed into a deep to get it digitised and into a computer start there and then tweak it. That is the (more than five layers) neural network. so they can make the analysis.’ world we are in right now. As computing Testing on non-trained samples This data could be collected at the power becomes more accessible, enabled researchers to create an ROC point, or it could be mailed off and that means we can experiment more,’ n curve, which is a graphical plot that scanned at another location. However, Ruderman concluded. illustrates the diagnostic ability of a Ruderman stressed that this should not binary classifier system. The initial area be seen as a replacement for traditional Dan Ruderman is assistant professor of under the curve (AOC) was 0.72. methods, rather it should be used to research medicine at the Keck School While initial results were promising, supplement and improve doctors ability of Medicine, and the Lawrence J Ellison several iterations of the network and to diagnose. Institute for Transformative Medicine, at advances in organisation, compression ‘For every cancer, there is an the University of Southern California www.scientific-computing.com/lig21 29 LABORATORY INFORMATICS GUIDE 2021 Safeguarding quality, empowering collaboration
Thermo Fisher Scientific’s Darren Barrington-Light highlights the need for standards as data volumes increase
cross all areas of the life inefficiencies and achieve the highest delay decisions, costing businesses sciences, the volume of standards of data integrity? valuable time and undermining A data handled by analytical organisational agility. laboratories has massively expanded. The challenge of managing data Additional challenges associated Thanks to improvements in the securely and efficiently with poorly integrated data capacity and speed of technologies For enterprise organisations with management systems centre around such as liquid chromatography laboratories situated across multiple compliance. With information stored (LC), gas chromatography (GC) and countries and even continents, on local computer terminals – in some mass spectrometry (MS), research commercial success depends on cases protected by a single user organisations are generating data on the seamless and secure flow of account used by the entire team – there an unprecedented scale. information between teams. With is a greater risk of unauthorised or At the same time, ongoing international supply chains, regional undocumented access. advances in bioinformatics tools, outsourcing partners and global Encountering these challenges in as well as data storage and centres of excellence, organisations just a single laboratory can be a major computational processing power, must act as one – there’s no room for headache. When you multiply these mean scientists can now derive more fragmented thinking when it comes to issues across an enterprise-level insight from a greater number of winning the competitive advantage. organisation, they become a serious samples, faster than ever before. The limitations of adopting threat to operational functionality. The expansion in the volume and a fragmented approach to data complexity of laboratory data has management are perhaps most Cloud-based CDS solutions: occurred alongside the growing apparent at the interface between Simplifying data sharing and normalisation of outsourcing and systems. While individual platforms collaboration strategic collaboration in the life might allow laboratories to perform Fortunately, modern cloud-based science sector, which involves the specific functions successfully, chromatography data system (CDS) sharing of data on a global scale. considerable manual effort is required software solutions are helping Simultaneously, regulatory when it comes to applying or sharing enterprise-level businesses to authorities have put additional focus this data downstream, including the overcome the challenges of disparate on the accuracy, consistency and transcription of data, conversion of file information management through traceability of this information to formats or navigation of complex folder integrating people, technologies and protect the safety of consumers and systems. workflows in a single system. By storing end-users. As such, it has become Not only are these efforts slow and chromatography and MS data centrally more important for organisations inefficient, but they also increase the in the cloud, these systems eliminate to have the right digital tools in potential for human error, putting the friction caused by using multiple place to collect, store, manage accuracy of data in jeopardy. Moreover, systems, allowing instant, secure and share laboratory data. But with if multiple copies of the same dataset sharing and access of information from aspects of information management are stored on individual local systems, any location. With a single source of challenging for even the smallest of sharing the most up-to-date version truth, all authorised individuals have laboratories, how can enterprise- between teams can cause confusion seamless access to the data they need, level organisations, with teams and waste valuable time and resources, helping teams spend more time on the working across several sites, optimise if discrepancies must be investigated tasks that add real value in workflows. their digital systems to minimise and resolved. Each of these issues can Furthermore, some of the latest
30 www.scientific-computing.com/lig21 LABORATORY INFORMATICS GUIDE 2021
CDS solutions are highly compatible with instruments from a wide range of “Storing chromatography and vendors, enabling teams to collaborate MS data centrally in the cloud, with whatever their legacy instruments. This enhanced flexibility also gives eliminates friction caused by using companies the freedom to invest in the multiple systems, allowing instant, best technologies available to them, unrestricted by vendor constraints, secure sharing and access of enabling full workflow scalability as information from any location” business needs change.
Upholding enhanced standards of data integrity and compliance In addition to streamlining workflows detailed audit trail, organisations can could be implemented ‘out-of-the-box’, and making collaboration more efficient, access an unambiguous source of and its broad customisability allowed cloud-based enterprise software is truth with which to demonstrate full for the solution to be perfectly tailored helping companies of all shapes and regulatory compliance. Thanks to the to meet the company’s needs across sizes safeguard the accuracy and powerful audit trail search functionality different business units. integrity of their laboratory data. By and version management tools in the Following a quick and hassle-free applying a single, flexible solution latest CDS packages, recalling specific implementation, the CDS enabled the across the organisation, businesses events or investigating non-compliant QC team to access their LC systems can standardise the way information behaviour is also quick and easy. remotely via a browser, integrating more is collected, processed and analysed, than 100 personnel across multiple supporting more consistent and reliable Assuring data integrity and boosting teams at different sites. outcomes. efficiency in biopharma One of the biggest advantages Human-introduced errors are a Given the benefits of bringing together of the new system for the QC team major source of frustration in the teams, instruments and processes, was the ability to eliminate computer analytical laboratory, potentially enterprise-level organisations terminals from the laboratory itself, causing out-of-specification data, operating across the life science sector freeing up valuable workspace to the need to re-run samples and, if are increasingly leveraging new CDS expand analytical capacity. As well as working in a regulated environment, software to streamline their workflows making the company’s laboratories additional documentation for regulatory and better protect the integrity of their more productive, this also strengthened authorities. This challenge can be data. their ability to uphold the highest particularly acute for laboratories One such organisation is a global, standards of data integrity by reducing with multiple chromatography and MS multi-site biotechnology company uncontrolled access to data across control systems, or workflows requiring focused on drug discovery and multiple workstations. Based on the extensive manual steps for data development. inherent scalability afforded by the processing or instrument set-up. With sites around the world, the cloud-based platform, the company Cloud-based data management business needed an efficient solution was able to expand its operations with systems are making data more that would seamlessly integrate minimal disruption, adding new LC controllable with the latest CDS users from across quality control, systems as required. solutions delivering a level of analytical development, and R&D Above all, the new cloud-based information security that’s a world laboratories. The platform had to CDS software increased organisational away from the spreadsheet and simplify and empower collaboration, flexibility, performance and productivity, paper-based workflows of the past. while maintaining robust data quality while reducing IT operation and The flexible user management and standards in their fast-paced regulated maintenance costs compared with on- secure access control features found laboratories. After considering their site data storage. in platforms like Thermo Scientific options, the company chose to As the volume of chromatography Chromeleon CDS, for example, allow implement Chromeleon CDS, with data and MS data expands, fragmented individuals to be assigned unique storage provided by Amazon Web approaches to information view and edit privileges, ensuring Services, and Amazon AppStream set management are putting effective individuals can only access and/ up to manage the applications. collaboration, operational efficiency or make changes to the information The biotechnology company worked and data integrity at risk. Thanks to they are entitled to. This capability closely with application specialists the latest cloud-based CDS solutions, is supplemented by electronic at Thermo Fisher Scientific, who enterprise organisations are integrating signatures, assuring compliance with developed a cloud-based system their digital systems to achieve high- n 21 CFR Part 11 requirements for the architecture that ensured all data could quality, compliant results. seamless implementation of paperless be securely stored off-site, while fully environments. meeting the needs of non-regulatory Darren Barrington-Light is senior product Also, by securely logging all user and regulatory compliant teams. The marketing manager, eCDS, Thermo Fisher interactions with the system in a platform’s flexibility meant the system Scientific
www.scientific-computing.com/lig21 31 LABORATORY INFORMATICS GUIDE 2021 Directory of suppliers
A list leading of suppliers, consultants and integrators
Abbott Informatics Achiever Medical LIMS Interactive Software Limited Abbott Informatics Europe Ltd. TS1, Pinewood Business Park, Crossgate House, Cross Street Coleshill Road, Solihull Sale, Manchester, M33 7FT, UK West Midlands, UK, B37 7HG Tel: +44 (0) 161 711 0340 Tel: +44 (0) 121 380 1010 [email protected] [email protected] www.informatics.abbott www.interactivesoftware.co.uk Abbott Informatics provides leading Laboratory Information Management Configurable, web-based Achiever Medical LIMS centralises lab data System (LIMS) solutions that have served customers around the world for more and supports the complex workflow and compliance needs of research than 30 years. STARLIMS solutions help improve the reliability of laboratory organisations, biobanks and biorepositories. The LIMS provides complete sampling processes, manage complex testing workflows, support compliance traceability and auditing of all sample lifecycle events and activities. A library with global regulatory requirements, and provide comprehensive reporting, of real-time, interactive dashboards tracking performance, bottlenecks and monitoring and analysis capabilities. trends is also included.
Advanced Chemistry Development, Autoscribe Informatics Inc. (ACD/Labs) 8 King Street East, Suite 107 1 Venus House, Calleva Park Toronto, ON M5C 1B5 Aldermaston, Reading Canada RG7 8DA, UK Tel: +1 (416) 368-3435 Tel: +44 (0) 118 984 0610 [email protected] l www.acdlabs.com [email protected] ACD/Labs is a leading provider of scientific software for R&D. We help our www.autoscribeinformatics.com customers assemble digitized analytical, structural, and molecular information for effective decision-making, problem solving, and product lifecycle control. Autoscribe Informatics offers industry leading configurable future-proof Our enterprise technologies enable automation of molecular characterization and LIMS software. With 30 years’ experience our solutions are configured facilitate chemically intelligent knowledge management. to match user requirements and can easily adapt as needs evolve. Matrix ACD/Labs provides worldwide sales and support, and brings 25 years of Gemini LIMS (LES, ELN & QMS) allows you to track and manage testing experience and success helping organizations innovate and create efficiencies in activities within a controlled environment with ease. their workflows.
BSSN Software Collaborative Drug Discovery, Inc. Nine Hills Road Wittichstraße 6 Cambridge, CB2 1JT 64295 Darmstadt, Germany United Kingdom Dr Peter Maier: +49 6151 78537 39 [email protected] Tel: +44 (0) 1223 803830 bssn-software.com [email protected] l www.collaborativedrug.com BSSN Software, owned by Merck KGaA, Darmstadt, Germany, develops Collaborative Drug Discovery, Inc. (www.collaborativedrug.com) flagship data management and informatics software to facilitate interoperability and product, CDD Vault, is a secure hosted platform for management and sharing data accessibility in the laboratory, enabling customers to process, analyze, of biological and chemical information. It enables researchers to intuitively archive, and share all their analytical and biological data. BSSN supports organize chemical structures and biological study data, and collaborate with open, modular, and vendor-neutral data solutions, and offers best-in-class partners through a straightforward web-interface. CDD Vault functionality consulting to assist our customers’ digital transformations. includes Activity, Registration, Visualization, Modelling, Inventory and ELN.
32 www.scientific-computing.com/lig21 Say ChEESE Subscribe for free*
Do you compute? The only global publication for scientists and engineers using computing and software in their daily work
Also published by Europa Science HPC 2020-2021 *Registration required
Do you subscribe? Register for free now! scientific-computing.com/subscribe LABORATORY INFORMATICS GUIDE 2021
Digital Lab Consulting Ltd Dotmatics
London, N1 7GU, United Kingdom Head Office UK North America East Coast Tel: +44 (0)1543 547607 The Old Monastery, Windhill, 500 West Cummings Park,Suites [email protected] Bishops Stortford,Herts, CM23 2ND 3750 & 3950, Woburn, MA 01801 www.dlc.io +44(0)1279 654 123 +1 855 808 8332 www.dotmatics.com/ Global Offices [email protected] www.dotmatics.com/about/contact
Digital Lab Consulting provides independent strategic and business Dotmatics is a global scientific informatics software and services company founded consulting services to enable organisations of all sizes to transform their in 2005. It is driving automation of laboratory workflows for discovery and business through better use of informatics. We provide clear, actionable innovation research in chemistry, biology and chemicals & materials organizations. advice to help companies find the most effective solution for their Capabilities include: knowledge management, ELN for chemistry, biology, analytical environment. & formulation, assay data management, lab data automation, biology and chemistry registration, inventory management, and visual data analytics.
LabWare iVention Lab Automation
Denzell Lodge, Dunham Road Wipstrikkerallee 95 204 South Floyd Street, Altrincham, Cheshire, WA14 4QE 8023 DW Zwolle Louisville,KY 40202, USA Tel: +44 161 927 5600 The Netherlands Tel: +1 (502) 909-0317 [email protected] Tel: +31 (0) 38 452 83 75 [email protected] www.labware.com [email protected] www.ivention.us www.ivention.nl LabWare’s Enterprise Laboratory Platform comprising LabWare LIMS & ELN/LES, continues to promote success with the latest release of LabWare 8 and its Mobile capabilities. As an integrated single solution it offers the industry’s broadest range Since its establishment in 2009, iVention has shaken up the market for of beneficial functionality and is based entirely on open standards. This provides Laboratory Information Management Systems. iVention’s iLES platform offers the best solution to current requirements and also enables the system to be readily laboratories a flexible software system designed around the laboratory process. It adapted as your business needs evolve. A wide range of pre-configured industry enables laboratories to streamline their workflow and manage and computerize templates are also available to help fast-track installations. LabWare focuses on customer success, providing a global support and services network backed by some their work, even in highly regulated environments. iLES is a powerful of the most experienced professionals in the world. management tool that allows significant efficiency and quality improvements.
MilliporeSigma Thermo Fisher Scientific
3050 Spruce St. Informatics St. Louis, MO 63103 USA 1600 Cherry Street Dr Haydn Boehm: +44 7866 116946 Philadelphia, PA 19102 [email protected] USA sigmaaldrich.com Tel: +1 (215) 964-6124 The life science business of Merck KGaA, Darmstadt, Germany is dedicated to www.thermofisher.com/informatics solving the industry’s toughest problems by collaborating with the global scientific Thermo Fisher Scientific has been providing state-of-the-art Integrated community. We provide scientists with lab materials, technologies and services to Informatics solutions for more than 30 years. Our portfolio includes the largest make research and biotech production simpler, faster and safer. MilliporeSigma global organizations across every industry, from pharma, food & beverage, acquired BSSN Software to empower their customers to better use and share their environmental and oil and gas, representing the broadest range of complex scientific data, and to build upon a growing portfolio of digital laboratory solutions. customer requirements related to integrated, enterprise-level informatics solutions.
Torx Software For news New Cambridge House, Bassingbourn Road, Litlington, Cambridgeshire, UK updates www.torx-software.com [email protected] direct from Improving the Design-Make-Test-Analyze cycle efficiency is a focal point of small the editorial molecule discovery programs and could reduce lead discovery and optimization time and cost. Torx is a re-imagined scientific workflow capturing all information throughout the DMTA cycle. Independent of therapeutic area or company size, team Torx can be integrated into your drug discovery workflow, to inspire collaborative SCIENTIFIC working and drive productivity. COMPUTING @scwmagazine WORLD
34 www.scientific-computing.com/lig21 Transform Digital Lab Consulting® provides independent strategic consulting to enable organisations of all sizes to transform their business through better use of informatics.
We provide clear, actionable advice to help companies find the most effective solution for their environment.
We have over 20 years of experience across the entire value chain, from early research to manufacturing.
We are based in the UK and work globally with our clients and partners.
Discover more at dlc.io
+44 (0)1543 547607 [email protected] LABWARE LIMS and ELN in a single platform Automation software for all laboratories
Offices worldwide supporting customers in more than 125 countries
www.labware.com