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Istls Information Services to Life Science Internet Bioinformatics Resources Josef Maier [E-Mail: [email protected]] Last Checked August, 17Th, 2011
IStLS Information Services to Life Science Internet Bioinformatics Resources Josef Maier [e-mail: [email protected]] Last checked August, 17th, 2011 IStLS Bioinformatics Resources http://www.istls.de/bioinfolinks.php Courses and lectures Bioinformatics - Online Courses and Tutorials http://www.bioinformatik.de/cgi-bin/browse/Catalog/Research_and_Education/Online_Courses_and_Tutorials/ EMBRACE Network of Excellence http://www.embracegrid.info/page.php EMBNet Quick Guides http://www.embnet.org/node/64 EMBNet Courses http://www.embnet.org/ Sequence Analysis with distributed Resources http://bibiserv.techfak.uni-bielefeld.de/sadr/ Tutorial Protein Structures (EXPASY) SwissModel http://swissmodel.expasy.org/course/course-index.htm CMBI Courses for protein structure http://swift.cmbi.ru.nl/teach/courses/index.html 2Can Support Portal - Bioinformatics educational resource http://www.ebi.ac.uk/2can Bioconductor Workshops http://www.bioconductor.org/workshops/ CBS Bioinformatics Courses http://www.cbs.dtu.dk/courses.php The European School In Bioinformatics (Biosapiens) http://www.biosapiens.info/page.php?page=esb Institutes Centers Networks Bioinformatics Institutes Germany WSI Wilhelm-Schickard-Institut für Informatik - Universitaet Tuebingen http://www.uni-tuebingen.de/en/faculties/faculty-of-science/departments/computer-science/department.html WSI Huson - Algorithms in Bioinformatics http://www-ab.informatik.uni-tuebingen.de/welcome.html WSI Prof. Zell - Computer Architecture http://www.ra.cs.uni-tuebingen.de/ WSI Kohlbacher - Div. for Simulation -
Practical Chemoinformatics Muthukumarasamy Karthikeyan • Renu Vyas
Practical Chemoinformatics Muthukumarasamy Karthikeyan • Renu Vyas Practical Chemoinformatics 1 3 Muthukumarasamy Karthikeyan Renu Vyas Digital Information Resource Centre Scientist (DST) National Chemical Laboratory Division of Chemical Engineering and Pune Process Development India National Chemical Laboratory Pune India ISBN 978-81-322-1779-4 ISBN 978-81-322-1780-0 (eBook) DOI 10.1007/978-81-322-1780-0 Springer New Delhi Dordrecht Heidelberg London New York Library of Congress Control Number: 2014931501 © Springer India 2014 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recita- tion, broadcasting, reproduction on microfilms or in any other physical way, and transmission or infor- mation storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar meth- odology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplica- tion of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher’s location, in its current version, and permission for use must always be obtained from Springer. Permissions for use may be obtained through RightsLink at the Copyright Clearance Center. Violations are liable to prosecution under the respective Copyright Law. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publica- tion does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. -
Open Data, Open Source, and Open Standards in Chemistry: the Blue Obelisk Five Years On" Journal of Cheminformatics Vol
Oral Roberts University Digital Showcase College of Science and Engineering Faculty College of Science and Engineering Research and Scholarship 10-14-2011 Open Data, Open Source, and Open Standards in Chemistry: The lueB Obelisk five years on Andrew Lang Noel M. O'Boyle Rajarshi Guha National Institutes of Health Egon Willighagen Maastricht University Samuel Adams See next page for additional authors Follow this and additional works at: http://digitalshowcase.oru.edu/cose_pub Part of the Chemistry Commons Recommended Citation Andrew Lang, Noel M O'Boyle, Rajarshi Guha, Egon Willighagen, et al.. "Open Data, Open Source, and Open Standards in Chemistry: The Blue Obelisk five years on" Journal of Cheminformatics Vol. 3 Iss. 37 (2011) Available at: http://works.bepress.com/andrew-sid-lang/ 19/ This Article is brought to you for free and open access by the College of Science and Engineering at Digital Showcase. It has been accepted for inclusion in College of Science and Engineering Faculty Research and Scholarship by an authorized administrator of Digital Showcase. For more information, please contact [email protected]. Authors Andrew Lang, Noel M. O'Boyle, Rajarshi Guha, Egon Willighagen, Samuel Adams, Jonathan Alvarsson, Jean- Claude Bradley, Igor Filippov, Robert M. Hanson, Marcus D. Hanwell, Geoffrey R. Hutchison, Craig A. James, Nina Jeliazkova, Karol M. Langner, David C. Lonie, Daniel M. Lowe, Jerome Pansanel, Dmitry Pavlov, Ola Spjuth, Christoph Steinbeck, Adam L. Tenderholt, Kevin J. Theisen, and Peter Murray-Rust This article is available at Digital Showcase: http://digitalshowcase.oru.edu/cose_pub/34 Oral Roberts University From the SelectedWorks of Andrew Lang October 14, 2011 Open Data, Open Source, and Open Standards in Chemistry: The Blue Obelisk five years on Andrew Lang Noel M O'Boyle Rajarshi Guha, National Institutes of Health Egon Willighagen, Maastricht University Samuel Adams, et al. -
Molecular Structure Input on the Web Peter Ertl
Ertl Journal of Cheminformatics 2010, 2:1 http://www.jcheminf.com/content/2/1/1 REVIEW Open Access Molecular structure input on the web Peter Ertl Abstract A molecule editor, that is program for input and editing of molecules, is an indispensable part of every cheminfor- matics or molecular processing system. This review focuses on a special type of molecule editors, namely those that are used for molecule structure input on the web. Scientific computing is now moving more and more in the direction of web services and cloud computing, with servers scattered all around the Internet. Thus a web browser has become the universal scientific user interface, and a tool to edit molecules directly within the web browser is essential. The review covers a history of web-based structure input, starting with simple text entry boxes and early molecule editors based on clickable maps, before moving to the current situation dominated by Java applets. One typical example - the popular JME Molecule Editor - will be described in more detail. Modern Ajax server-side molecule editors are also presented. And finally, the possible future direction of web-based molecule editing, based on tech- nologies like JavaScript and Flash, is discussed. Introduction this trend and input of molecular structures directly A program for the input and editing of molecules is an within a web browser is therefore of utmost importance. indispensable part of every cheminformatics or molecu- In this overview a history of entering molecules into lar processing system. Such a program is known as a web applications will be covered, starting from simple molecule editor, molecular editor or structure sketcher. -
Spoken Tutorial Project, IIT Bombay Brochure for Chemistry Department
Spoken Tutorial Project, IIT Bombay Brochure for Chemistry Department Name of FOSS Applications Employability GChemPaint GChemPaint is an editor for 2Dchem- GChemPaint is currently being developed ical structures with a multiple docu- as part of The Chemistry Development ment interface. Kit, and a Standard Widget Tool kit- based GChemPaint application is being developed, as part of Bioclipse. Jmol Jmol applet is used to explore the Jmol is a free, open source molecule viewer structure of molecules. Jmol applet is for students, educators, and researchers used to depict X-ray structures in chemistry and biochemistry. It is cross- platform, running on Windows, Mac OS X, and Linux/Unix systems. For PG Students LaTeX Document markup language and Value addition to academic Skills set. preparation system for Tex typesetting Essential for International paper presentation and scientific journals. For PG student for their project work Scilab Scientific Computation package for Value addition in technical problem numerical computations solving via use of computational methods for engineering problems, Applicable in Chemical, ECE, Electrical, Electronics, Civil, Mechanical, Mathematics etc. For PG student who are taking Physical Chemistry Avogadro Avogadro is a free and open source, Research and Development in Chemistry, advanced molecule editor and Pharmacist and University lecturers. visualizer designed for cross-platform use in computational chemistry, molecular modeling, material science, bioinformatics, etc. Spoken Tutorial Project, IIT Bombay Brochure for Commerce and Commerce IT Name of FOSS Applications / Employability LibreOffice – Writer, Calc, Writing letters, documents, creating spreadsheets, tables, Impress making presentations, desktop publishing LibreOffice – Base, Draw, Managing databases, Drawing, doing simple Mathematical Math operations For Commerce IT Students Drupal Drupal is a free and open source content management system (CMS). -
Designing Universal Chemical Markup (UCM) Through the Reusable Methodology Based on Analyzing Existing Related Formats
Designing Universal Chemical Markup (UCM) through the reusable methodology based on analyzing existing related formats Background: In order to design concepts for a new general-purpose chemical format we analyzed the strengths and weaknesses of current formats for common chemical data. While the new format is discussed more in the next article, here we describe our software s t tools and two stage analysis procedure that supplied the necessary information for the n i r development. The chemical formats analyzed in both stages were: CDX, CDXML, CML, P CTfile and XDfile. In addition the following formats were included in the first stage only: e r P CIF, InChI, NCBI ASN.1, NCBI XML, PDB, PDBx/mmCIF, PDBML, SMILES, SLN and Mol2. Results: A two stage analysis process devised for both XML (Extensible Markup Language) and non-XML formats enabled us to verify if and how potential advantages of XML are utilized in the widely used general-purpose chemical formats. In the first stage we accumulated information about analyzed formats and selected the formats with the most general-purpose chemical functionality for the second stage. During the second stage our set of software quality requirements was used to assess the benefits and issues of selected formats. Additionally, the detailed analysis of XML formats structure in the second stage helped us to identify concepts in those formats. Using these concepts we came up with the concise structure for a new chemical format, which is designed to provide precise built-in validation capabilities and aims to avoid the potential issues of analyzed formats. -
Open Data, Open Source and Open Standards in Chemistry: the Blue Obelisk five Years On
Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk ¯ve years on Noel M O'Boyle¤1 , Rajarshi Guha2 , Egon L Willighagen3 , Samuel E Adams4 , Jonathan Alvarsson5 , Richard L Apodaca6 , Jean-Claude Bradley7 , Igor V Filippov8 , Robert M Hanson9 , Marcus D Hanwell10 , Geo®rey R Hutchison11 , Craig A James12 , Nina Jeliazkova13 , Andrew SID Lang14 , Karol M Langner15 , David C Lonie16 , Daniel M Lowe4 , J¶er^omePansanel17 , Dmitry Pavlov18 , Ola Spjuth5 , Christoph Steinbeck19 , Adam L Tenderholt20 , Kevin J Theisen21 , Peter Murray-Rust4 1Analytical and Biological Chemistry Research Facility, Cavanagh Pharmacy Building, University College Cork, College Road, Cork, Co. Cork, Ireland 2NIH Center for Translational Therapeutics, 9800 Medical Center Drive, Rockville, MD 20878, USA 3Division of Molecular Toxicology, Institute of Environmental Medicine, Nobels vaeg 13, Karolinska Institutet, 171 77 Stockholm, Sweden 4Unilever Centre for Molecular Sciences Informatics, Department of Chemistry, University of Cambridge, Lens¯eld Road, CB2 1EW, UK 5Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, Sweden 6Metamolecular, LLC, 8070 La Jolla Shores Drive #464, La Jolla, CA 92037, USA 7Department of Chemistry, Drexel University, 32nd and Chestnut streets, Philadelphia, PA 19104, USA 8Chemical Biology Laboratory, Basic Research Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702, USA 9St. Olaf College, 1520 St. Olaf Ave., North¯eld, MN 55057, USA 10Kitware, Inc., 28 Corporate Drive, Clifton Park, NY 12065, USA 11Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260, USA 12eMolecules Inc., 380 Stevens Ave., Solana Beach, California 92075, USA 13Ideaconsult Ltd., 4.A.Kanchev str., So¯a 1000, Bulgaria 14Department of Engineering, Computer Science, Physics, and Mathematics, Oral Roberts University, 7777 S. -
(CDK): an Open-Source Java Library for Chemo- and Bioinformatics
J. Chem. Inf. Comput. Sci. 2003, 43, 493-500 493 The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics Christoph Steinbeck,*,† Yongquan Han,† Stefan Kuhn,† Oliver Horlacher,‡ Edgar Luttmann,§ and Egon Willighagen# Max-Planck-Institute of Chemical Ecology, Jena, Germany, TheraSTrat AG, Allschwil, Switzerland, Institute of Organic Chemistry, University of Paderborn, Germany, and Nijmegen, The Netherlands Received August 17, 2002 The Chemistry Development Kit (CDK) is a freely available open-source Java library for Structural Chemo- and Bioinformatics. Its architecture and capabilities as well as the development as an open-source project by a team of international collaborators from academic and industrial institutions is described. The CDK provides methods for many common tasks in molecular informatics, including 2D and 3D rendering of chemical structures, I/O routines, SMILES parsing and generation, ring searches, isomorphism checking, structure diagram generation, etc. Application scenarios as well as access information for interested users and potential contributors are given. 1. INTRODUCTION of software development, most widely recognized through the great success of the free Unix-like operating system Whoever pursues the endeavor of creating a larger GNU/Linux, a collaborative work of many individuals and software package in chemoinformatics or computational organizations, including the Free Software Foundation lead chemistry from scratch will soon be confronted with the by Richard Stallman and the Finish computer science student Syssiphus task of implementing the standard repertoire of Linus Torvalds who started the project. According to several chemoinformatical algorithms and components invented essays on this subject, open-source software, for which, by during the last 20 or 30 years. -
JUMBO Is an Opensource Toolkit Addressing the Semantic and Ontological Impedances That Are Major Barriers to Interoperability in Computational Chemistry and Physics
a a c a b a a c d a b c d JUMBO is an OpenSource toolkit addressing the semantic and ontological impedances that are major barriers to interoperability in computational chemistry and physics. Users build XMLSchemas from generic XML components to support particular computational tasks, such as high-throughput chemistry. JUMBO components provide a complete semantic description of information to or from a code such as MOPAC or GAMESS. Codes are edited to use JUMBO libraries as adapters to program-independent XML objects, or output is transduced using a generic parser, JUMBOMarker. The JUMBO system is designed for flexible collaborative contributions. abstract and rely on dictionaries (v.i.) to add semantics and ontology. In practice many of the concepts in a program are not in the schema but Existing codes in quantum mechanics or provided by domain-specific dictionaries. crystal/molecular mechanics/dynamics rely on The ultimate goal is to provide simple and “FORTRAN-like” input and output with flexible tools to XMLise existing and future variable and misunderstandable semantics and computational codes so they can be used as ontology. Typical examples are the lack of “black-boxes” in eScience workflows. Some explicit scientific units or fuzziness over authors have adopted this approach and whether a molecule has a charge. It is difficult embedded calls to JUMBO libraries in their to chain the output of one program into the code for input and output. However in some input of the next so human “cut-and-paste” is cases native legacy methods must still be used frequent. JUMBO allows authors and users to (for example where we do not have access or wrap these codes in XML and convert them to permission to modify source). -
Openchrom: a Cross-Platform Open Source Software for the Mass Spectrometric Analysis of Chromatographic Data Philip Wenig*, Juergen Odermatt
Wenig and Odermatt BMC Bioinformatics 2010, 11:405 http://www.biomedcentral.com/1471-2105/11/405 SOFTWARE Open Access OpenChrom: a cross-platform open source software for the mass spectrometric analysis of chromatographic data Philip Wenig*, Juergen Odermatt Abstract Background: Today, data evaluation has become a bottleneck in chromatographic science. Analytical instruments equipped with automated samplers yield large amounts of measurement data, which needs to be verified and analyzed. Since nearly every GC/MS instrument vendor offers its own data format and software tools, the consequences are problems with data exchange and a lack of comparability between the analytical results. To challenge this situation a number of either commercial or non-profit software applications have been developed. These applications provide functionalities to import and analyze several data formats but have shortcomings in terms of the transparency of the implemented analytical algorithms and/or are restricted to a specific computer platform. Results: This work describes a native approach to handle chromatographic data files. The approach can be extended in its functionality such as facilities to detect baselines, to detect, integrate and identify peaks and to compare mass spectra, as well as the ability to internationalize the application. Additionally, filters can be applied on the chromatographic data to enhance its quality, for example to remove background and noise. Extended operations like do, undo and redo are supported. Conclusions: OpenChrom is a software application to edit and analyze mass spectrometric chromatographic data. It is extensible in many different ways, depending on the demands of the users or the analytical procedures and algorithms. It offers a customizable graphical user interface. -
On the Redundancy of Natural Products Public Databases and Where to Find Data in 2020 - a Review on Natural Products Databases
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 25 December 2019 doi:10.20944/preprints201912.0332.v1 On the redundancy of natural products public databases and where to find data in 2020 - a review on natural products databases Dr. Maria Sorokina (ORCID 0000-0001-9359-7149) Prof. Dr. Christoph Steinbeck (ORCID 0000-0001-6966-0814) Institute for Inorganic and Analytical Chemistry Friedrich-Schiller-University Lessingstr. 8 07743 Jena Abstract Natural products (NPs) have been the centre of attention of the scientific community in the last decencies and the interest around them continues to grow incessantly. As a consequence, in the last 20 years, there was a rapid multiplication of various databases and collections as generalistic or thematic resources for NP information. In this review, we establish a complete overview of these resources, and the numbers are overwhelming: over 120 different NP databases and collections were published and re-used since 2000. 98 of them are still somehow accessible and only 50 are open access. The latter include not only databases but also big collections of NPs published as supplementary material in scientific publications and collections that were backed up in the ZINC database for commercially-available compounds. Some databases, even published relatively recently are already not accessible anymore, which leads to a dramatic loss of data on NPs. The data sources are presented in this manuscript, together with the comparison of the content of open ones. With this review, we also compiled the open-access natural compounds in one single dataset a COlleCtion of Open NatUral producTs (COCONUT), which is available on Zenodo and contains structures and sparse annotations for over 400000 non-redundant NPs, which makes it the biggest open collection of NPs available to this date. -
Optimizing the Use of Open-Source Software Applications in Drug
DDT • Volume 11, Number 3/4 • February 2006 REVIEWS TICS INFORMA Optimizing the use of open-source • software applications in drug discovery Reviews Werner J. Geldenhuys1, Kevin E. Gaasch2, Mark Watson2, David D. Allen1 and Cornelis J.Van der Schyf1,3 1Department of Pharmaceutical Sciences, School of Pharmacy,Texas Tech University Health Sciences Center, Amarillo,TX, USA 2West Texas A&M University, Canyon,TX, USA 3Pharmaceutical Chemistry, School of Pharmacy, North-West University, Potchefstroom, South Africa Drug discovery is a time consuming and costly process. Recently, a trend towards the use of in silico computational chemistry and molecular modeling for computer-aided drug design has gained significant momentum. This review investigates the application of free and/or open-source software in the drug discovery process. Among the reviewed software programs are applications programmed in JAVA, Perl and Python, as well as resources including software libraries. These programs might be useful for cheminformatics approaches to drug discovery, including QSAR studies, energy minimization and docking studies in drug design endeavors. Furthermore, this review explores options for integrating available computer modeling open-source software applications in drug discovery programs. To bring a new drug to the market is very costly, with the current of combinatorial approaches and HTS. The addition of computer- price tag approximating US$800 million, according to data reported aided drug design technologies to the R&D approaches of a com- in a recent study [1]. Therefore, it is not surprising that pharma- pany, could lead to a reduction in the cost of drug design and ceutical companies are seeking ways to optimize costs associated development by up to 50% [6,7].