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egonw created branch master at egonw/csrml-schema - https://github.com/egonw...
egonw created branch master at egonw/csrml-schema
egonw pushed to master at egonw/csrml-schema - https://github.com/egonw...
egonw pushed to master at egonw/csrml-schema
egonw pushed to master at egonw/csrml-schema - https://github.com/egonw...
egonw pushed to master at egonw/csrml-schema
egonw created repository egonw/csrml-schema - https://github.com/egonw...
egonw created repository egonw/csrml-schema
egonw pushed to master at egonw/csrml-schema - https://github.com/egonw...
egonw pushed to master at egonw/csrml-schema
A New Publicly Available Chemical Query Language, CSRML, to support Chemotype Representations for Application to Data Mining and Modeling - http://www.citeulike.org/user...
J. Chem. Inf. Model. (3 February 2015), doi:10.1021/ci500667v Chemotypes are a new approach for representing molecules, chemical substructures and patterns, reaction rules, and reactions. Chemotypes are capable of integrating types of information beyond what is possible using current representation methods (e.g., SMARTS patterns) or reaction transformations (e.g., SMIRKS, reaction SMILES). Chemotypes are expressed in the XML-based Chemical Subgraphs and Reactions Mark-up Language (CSRML), and can be encoded not only with connectivity and topology, but also with properties of atoms, bonds, electronic systems, or molecules. The CSRML language has been developed in parallel with a public set of chemotypes, i.e., the ToxPrint chemotypes, which are designed to provide excellent coverage of environmental, regulatory and commercial-use chemical space, as well as to represent chemical patterns and properties especially relevant to various toxicity concerns. A software application, ChemoTyper... - Egon Willighagen
A M.Sc. thesis can be cited too, if stored and available! +Samuel Lampa's thesis resulted in this reuse... - https://plus.google.com/1041867...
A M.Sc. thesis can be cited too, if stored and available! +Samuel Lampa's thesis resulted in this reuse from Jan Wielemaker et al. in Amsterdam: "The Blipkit [18] system is a comprehensive system for querying and transforming data in bioinformatics. Blipkit’s RDF support in terms of performance and expressiveness was evaluated by Lampa [15]. Lampa stresses the enhanced maintainability of Prolog queries due to reuse of query fragments represented as predicates (Figure 18 in [15])." http://uu.diva-portal.org/smash... BTW, did you see those download counts?? If only DIVA used DOIs... Lampa, Samuel. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. (Prof. Jarl Wikberg, Bioclipse group). 2010 (English)Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis ... - Egon Willighagen
Well, clearly the +American Chemical Society hasn't solved the cookie issue with their journals yet,... - https://plus.google.com/1041867...
Well, clearly the +American Chemical Society hasn't solved the cookie issue with their journals yet, but this is a paper by a large group of well-known cheminformaticians. The work seems interesting and will get back on the details. This is certainly a paper I like to review (in my blog and probably +Publons... it's about a proposed standard for substructure search specification. The CDK is used via the +KNIMETV nodes for the MACCS keys. The CDK website is cited, but none of the papers. Not for KNIME either, BTW. An Error Occurred Setting Your User Cookie. Your browser is currently set to not accept cookies. Please enable cookies in your web browser to continue. How do I enable cookies? For most browsers, the cookies settings are located under Preferences or Internet Options. - Egon Willighagen
Reshared post from Egon Willighagen: - https://plus.google.com/1041867...
Original Post from Egon Willighagen: Well, clearly the +American Chemical Society hasn't solved the cookie issue with their journals yet, but this is a paper by a large group of well-known cheminformaticians. The work seems interesting and will get back on the details. This is certainly a paper I like to review (in my blog and probably +Publons... it's about a proposed standard for substructure search specification. The CDK is used via the +KNIMETV nodes for the MACCS keys. The CDK website is cited, but none of the papers. Not for KNIME either, BTW. An Error Occurred Setting Your User Cookie. Your browser is currently set to not accept cookies. Please enable cookies in your web browser to continue. How do I enable cookies? For most browsers, the cookies settings are located under Preferences or Internet Options. - Egon Willighagen
A Quick Guide for Building a Successful Bioinformatics Community - http://www.citeulike.org/user...
PLoS Comput Biol, Vol. 11, No. 2. (5 February 2015), e1003972, doi:10.1371/journal.pcbi.1003972 “Scientific community” refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role in many bioinformatics activities. Communities may be linked to a specific location or institute, or involve people working at many different institutions and locations. Education and training is typically an important component of these communities, providing a valuable context in which to develop skills and expertise, while also strengthening links and relationships within the community. Scientific communities facilitate: (i) the exchange and development of ideas and expertise; (ii) career development; (iii) coordinated funding activities; (iv) interactions and engagement with professionals from other fields; and (v) other activities beneficial to individual participants, communities, and... - Egon Willighagen
Programming: Pick up Python - http://www.citeulike.org/user...
Nature, Vol. 518, No. 7537. (4 February 2015), pp. 125-126, doi:10.1038/518125a Jeffrey Perkel - Egon Willighagen
egonw created branch update/newRestService at egonw/cytoscape-wikipathways-app - https://github.com/egonw...
egonw created branch update/newRestService at egonw/cytoscape-wikipathways-app
egonw forked wikipathways/cytoscape-wikipathways-app to egonw/cytoscape-wikipathways-app - https://github.com/egonw...
egonw forked wikipathways/cytoscape-wikipathways-app to egonw/cytoscape-wikipathways-app
Our research school has a new logo. - https://plus.google.com/1041867...
Our research school has a new logo. As of January 2015 NUTRIM's name was changed into NUTRIM School of Nutrition and Translational Research in Metabolism. - Egon Willighagen
egonw closed issue BiGCAT-UM/wp2lod#2 - https://github.com/BiGCAT-...
egonw closed issue BiGCAT-UM/wp2lod#2
egonw pushed to master at BiGCAT-UM/wp2lod - https://github.com/BiGCAT-...
egonw pushed to master at BiGCAT-UM/wp2lod
egonw pushed to fix/soapRemoval at BiGCAT-UM/wp2lod - https://github.com/BiGCAT-...
egonw pushed to fix/soapRemoval at BiGCAT-UM/wp2lod
egonw pushed to fix/soapRemoval at BiGCAT-UM/wp2lod - https://github.com/BiGCAT-...
egonw pushed to fix/soapRemoval at BiGCAT-UM/wp2lod
egonw pushed to fix/soapRemoval at BiGCAT-UM/wp2lod - https://github.com/BiGCAT-...
egonw pushed to fix/soapRemoval at BiGCAT-UM/wp2lod
egonw pushed to fix/soapRemoval at BiGCAT-UM/wp2lod - https://github.com/BiGCAT-...
egonw pushed to fix/soapRemoval at BiGCAT-UM/wp2lod
egonw pushed to fix/soapRemoval at BiGCAT-UM/wp2lod - https://github.com/BiGCAT-...
egonw pushed to fix/soapRemoval at BiGCAT-UM/wp2lod
egonw created branch fix/soapRemoval at BiGCAT-UM/wp2lod - https://github.com/BiGCAT-...
egonw created branch fix/soapRemoval at BiGCAT-UM/wp2lod
egonw opened issue BiGCAT-UM/wp2lod#2 - https://github.com/BiGCAT-...
egonw opened issue BiGCAT-UM/wp2lod#2
egonw closed pull request cdk/cdk#115 - https://github.com/cdk...
egonw closed pull request cdk/cdk#115
egonw commented on pull request cdk/cdk#115 - https://github.com/cdk...
egonw commented on pull request cdk/cdk#115
egonw pushed to master at cdk/cdk - https://github.com/cdk...
egonw pushed to master at cdk/cdk
egonw pushed to master at egonw/cdk - https://github.com/egonw...
egonw pushed to master at egonw/cdk
Reshared post from Greg Landrum: - https://plus.google.com/1041867...
I like the $$$$ at the end... pharma product, I assume? :) Original Post from Greg Landrum: The new ChEMBL is here. Excellent! We are pleased to announce the release of ChEMBL_20. This version of the database was prepared on 14th January 2015 and contains: 1715135 compound records; 1463270 compounds (of which 1456020 have mol files); 13520737 activities; 1148942 assays; 10774 targets; 59610 source documents ... - Egon Willighagen
Pathway databases and tools for their exploitation: benefits, current limitations and challenges - http://www.citeulike.org/user...
Molecular Systems Biology, Vol. 5, No. 1. (28 July 2009), doi:10.1038/msb.2009.47 In past years, comprehensive representations of cell signalling pathways have been developed by manual curation from literature, which requires huge effort and would benefit from information stored in databases and from automatic retrieval and integration methods. Once a reconstruction of the network of interactions is achieved, analysis of its structural features and its dynamic behaviour can take place. Mathematical modelling techniques are used to simulate the complex behaviour of cell signalling networks, which ultimately sheds light on the mechanisms leading to complex diseases or helps in the identification of drug targets. A variety of databases containing information on cell signalling pathways have been developed in conjunction with methodologies to access and analyse the data. In principle, the scenario is prepared to make the most of this information for the analysis of the dynamics of... - Egon Willighagen
MetNetAPI: A flexible method to access and manipulate biological network data from MetNet - http://www.citeulike.org/user...
BMC Research Notes, Vol. 3, No. 1. (18 November 2010), 312, doi:10.1186/1756-0500-3-312 Convenient programmatic access to different biological databases allows automated integration of scientific knowledge. Many databases support a function to download files or data snapshots, or a webservice that offers "live" data. However, the functionality that a database offers cannot be represented in a static data download file, and webservices may consume considerable computational resources from the host server. Yves Sucaet, Eve Wurtele - Egon Willighagen
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