Title LABIRE - Latin American BIoinformatics REsource Lead Applicant Dr Adrian Turjanski Details of proposal – team members and collaborators Adrian Turjanski: Buenos Aires University. Argentinian Genomics data System (SNDG): Group Coordinator. Previous experience with similar systems César Rodríguez Sánchez: University of Costa Rica: Microbiology Expert. Key User Edgar Carvalho : Universidad Fedetal da Bahia: Negleted Diseases Exptert Guy Cochrane: EBI Team Leader – Compare Project initiative. Bioinformatics infrastructure Expert Key Collaborator: Cath Brooksbank: EBI – CABANA Project coodinator. Training and course management Expert Details of proposal – vision, aims and influence on open research Our vision is to provide a bioinformatics resource that allows storage and analysis of locally isolated pathogen genomes to fight communicable diseases. We want to create a Latin American hub for collaboration between health institutions to foster translational bioinformatics. We aim to create a Latin America database for communicable disease analysis and surveillance. This resource will provide standard based, ready to use, bioinformatics pipelines to analyze pathogen genomes. Such a system will benefit those tackling individual problems at the frontline, clinicians, as well as policy-makers. It will provide a web resource to identify and analyze outbreaks, resistant strains, compare genomes, allow to add metadata, and share the information to international resources. We will catalog Latin America data, tools, researchers and groups to allow collaborations between health institutions and bioinformaticians. Latin America needs to find solutions to fight communicable diseases and pathogens such as chagas, leishmaniasis, malaria, tuberculosis and dengue. Understanding the genomic makeup of local pathogen strains and sequence variations can have a major impact on clinical research, surveillance and diagnostic. However, international databases lack Latin America data both because is not well annotated and health institutions do not have bioinformaticians and personnel trained to analyze it. On the other hand, there is a new generation of bioinformaticians working in latinamerican research institutions that are developing tools to analyze genomic data. Finally, local governments lack a resource that allows them to know what data is generated and how resources need to be allocated to foster research in communicable diseases. The idea of connecting local bioinformaticians with health researchers is to have a sustainable development that can not be achieved by international collaboration alone. By developing a user- friendly web resource that allows sharing and processing locally obtained data through well- established pipelines will enhance distribution of not previously available local datasets. For the first, we will reuse the current National Genomic System currently function in Argentina, so can be extended to the rest of the region. In this way, much of the effort has to be done in the consolidation of the Latam network rather than a development from the scratch initiative. By making local datasets open and easy explorable, our project will encourage open research practices in Latinoamerica. The following activities will take place in the scope of the first year: 1) Software development: Currently SNDG and TargetPathogen supports genome, gene and structure searching and visualization. The engine behind those platforms will be extended to support user/group/country management, pan genome analysis (using panX), outbreak surveillance, genotypic resistance profile and comparative genomics (with GMOD or equivalent tools). Also standard pipelines must be ready to use to motivate local datasets upload and analysis. For example, process a group of samples to get sequence variability and resistance profiles. This would be carried out by a workflow management system such as Galaxy. As pilot project we will upload and process 200 Clostridium genomes from Costa Rica with the developed platform. 2) Meeting: An expert meeting formed by the team members, key collaborators and researchers of other recruited institutions would be held within the first three months of the project to define relevant pipeline guidelines and good practices for the platform use. In this meeting we will also discuss and establish how to disseminate the initiative. 3) Workshop: A training workshop would be held in November 2020, with attendees from the team, key collaborators and other recruited institutions. There we plan to debut the first release of our planned software framework to the community so that we can solicit feedback and encourage contributions. Details of proposal – evaluation plan The project progress will be evaluated by the success of the following goals according to schedule. Implementation of the platform with all the proposed features. The success of this goal will be tested by a pilot project performed by the available local Clostridium genomes provided by César Rodríguez Sánchez. (A) Adoption of the platform by the seed group to upload and analyse their own local datasets. This goal will be achieved if the institutions represented by the seed group actively upload and share datasets with the platform environment. (B) Recruitment of a seed group of at least 10 researchers of diverse Latinoamercican countries. This goal will be tested by the success of a first meeting with our team, key collaborators and new recruited researchers for the initiative. Platform adoption beyond the seed group. The two key success indicators of this goal will be the adoption of the developed platform by research and health care organizations of Latinoamerica to upload and analyse local datasets and a solid community engagement to broaden its scope beyond the lifetime of the grant. Decision Not shortlisted Comment on decision from Wellcome This was a potentially impactful proposal with a good evaluation plan. However the level of innovation proposed was limited. Title Using Natural Language Processing on all existing Open Access scientific publications to form the framework of the Octopus publishing platform Lead Applicant Dr Alexandra Freeman Details of proposal – team members and collaborators The applicant opted not to share this information Details of proposal – vision, aims and influence on open research The applicant opted not to share this information Details of proposal – evaluation plan The applicant opted not to share this information Decision Not shortlisted Comment on decision from Wellcome The applicant opted not to share this information Title Piloting the use of transformative agreements in the NHS to accelerate the transition to immediate Open Access Lead Applicant Dr Alicia Wise Details of proposal – team members and collaborators The applicant opted not to share this information Details of proposal – vision, aims and influence on open research The applicant opted not to share this information Details of proposal – evaluation plan The applicant opted not to share this information Decision Not shortlisted Comment on decision from Wellcome The applicant opted not to share this information Title Increasing access to open source spatial demographic data using worldpopR and QGIS plug-ins Lead Applicant Dr Andrew Tatem Details of proposal – team members and collaborators Andrew Tatem (WorldPop Director) supervise the project development and delivery, integrate outputs with GRID3 capacity strengthening efforts Natalia Tejedor Garavito (WorldPop Geospatial Data Technical Lead) Coordinate workshops and assist project delivery Maksym Bondarenko (WorldPop Spatial Data Infrastructure Lead) Deliver the R/Python packages and QGIS plug-in Alessandra Carioli (WorldPop R and Demographer) Provide expertise on the building of the R package and data visualization from a demographic perspective Pulane Tlebere (UNFPA) Implementation partner to convene health ministry representatives to take part in workshops to evaluate the outputs Details of proposal – vision, aims and influence on open research Vision: Enabling non-technical experts to use WorldPop spatial demographic data and integrate it into workflows to support health research and decision-making. Background: WorldPop (www.worldpop.org) provides a wide array of open access spatial demographic data, which are widely used by scientists and decision makers across the globe, particularly in low- and middle-income settings. These include geospatial datasets with estimates of population distributions, demographics and dynamics at 1x1km grid squares or finer, with the mapping of women of childbearing age, pregnancies and live births recently funded by the Wellcome Trust. These geospatial datasets have proven valuable to researchers and implementers in health and social research (>10,000 citations, >500,000 downloads), particularly in the field of health metrics, spatial epidemiology and in tracking progress towards development goals, where the use subnational data is increasingly emphasised. However, often the software required to analyse and visualise such geospatial data, such as ArcGIS, are often not open to researchers and practitioners, requiring expensive licenses and significantly limiting the range of data applications, particularly for low- and middle-income countries with insufficient computational resources. This makes it difficult for researchers and health practitioners to use the data, in addition to a general lack of expertise in many cases in ArcGIS and/or coding. In this context, R-Cran, Python and QGIS are