http://www.straininfo.net/docs/ 2012-05-18T06:01:30+02:00 http://www.straininfo.net/docs/ http://www.straininfo.net/docs/lib/images/favicon.ico text/html 2010-01-14T10:46:37+02:00 http://www.straininfo.net/docs/about?rev=1263462397&do=diff You can use StrainInfo to search through the catalogs of over 60 BRCs. Please note that StrainInfo is still in BETA phase. This means that not everything is fully streamlined or complete yet. In case you encounter errors, please do not hesitate to contact us. text/html 2010-02-16T16:57:58+02:00 http://www.straininfo.net/docs/advancedsearch?rev=1266335878&do=diff Advanced search allows building complex search queries. When multiple criteria are entered, they are combined. type strains only Strain Number e.g. "ATCC 18824" normalized Taxonomic Name e.g. "Staphylococcus aureus" include subtaxa INSDC Accession Number e.g. "AE016877" Full Text e.g. "dairy" The Full Text search is available only for content that was synchronized by XML. text/html 2010-01-14T11:02:39+02:00 http://www.straininfo.net/docs/amigos?rev=1263463359&do=diff The following colleagues have made (and continue to do so) substantial contributions or gave us inspirational suggestions that were incorporated into the strategy, design and implementation of StrainInfo: * Mohamed Amar Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Morocco * David Ruiz Arahal Coleccion Española de Cultivos Tipo, Spain * Michael Ashburner Department of Genetics, University of Cambridge, UK * Chri… text/html 2011-12-02T13:38:56+02:00 http://www.straininfo.net/docs/cite?rev=1322829536&do=diff When using StrainInfo for research please consider citing the following paper: * Dawyndt, P.; Vancanneyt, M.; De Meyer, H.; Swings, J., Knowledge accumulation and resolution of data inconsistencies during the integration of microbial information sources, IEEE Transactions on Knowledge and Data Engineering, vol.17, no.8, pp. 1111-1126, Aug. 2005 text/html 2011-12-02T13:38:56+02:00 http://www.straininfo.net/docs/conferences?rev=1322829536&do=diff Past conferences * Analysing Patterns of Exchange and Use in the Global Microbial Commons, Second Workshop., F.R.S.- FNRS (Fonds de la Recherche Scientifique), Brussels, Belgium, 25-26 March 2009. * 4th IEEE International Conference on e-Science, University Place Conference Center &amp; Hotel, Indianapolis, IN, USA, 7-12 December 2008. * Genomic Standards Consortium workshop, European Bioinformatics Institute (EBI), Cambridge, UK, 15-17 October 2008. * IUMS 2008 – Meetings of the Three … text/html 2010-01-14T12:27:48+02:00 http://www.straininfo.net/docs/contact?rev=1263468468&do=diff The StrainInfo team can be contacted via email: <StrainInfo@UGent.be>. Refer to the team members page for the contact details of individual team members. Project lead Prof. Dr. Peter Dawyndt Department of Applied Mathematics and Computer Science, Ghent University Krijgslaan 281 S9, 9000 Gent, Belgium text/html 2010-01-14T14:43:13+02:00 http://www.straininfo.net/docs/entrez?rev=1263476593&do=diff The Entrez Global Query Cross-Database Search System is a powerful federated search engine that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website. NCBI is part of the National Library of Medicine (NLM), itself a department of the National Institutes of Health (NIH) of the United States. Entrez Global Query is an integrated search and retrieval system that provides access to all databases simultaneously with a single… text/html 2011-12-02T13:38:56+02:00 http://www.straininfo.net/docs/exports?rev=1322829536&do=diff This page contains information on static exports. StrainInfo can also be accessed through its webservice interface. Public exports Available here Exports on request If you need specific information and there is no suitable export available, please contact us. text/html 2010-01-14T13:32:56+02:00 http://www.straininfo.net/docs/faq?rev=1263472376&do=diff Can I order strain XYZ 123? No. It is not possible to order strains from StrainInfo. StrainInfo is only a global catalog integrating the catalogs of culture collections worldwide giving uniform access to underlying collections. You have to order the strain from one of those collections. You can find all culture collections where the strain is available by searching for the strain. We can not make any suggestions regarding selecting a culture collection, but we suggest you use the map feature to… text/html 2010-01-13T16:54:35+02:00 http://www.straininfo.net/docs/foo?rev=1263398075&do=diff this is foo text/html 2010-05-06T16:51:43+02:00 http://www.straininfo.net/docs/help?rev=1273157503&do=diff About StrainInfo * About StrainInfo Information for users * What is StrainInfo? * Histri * Using the Histri Editor * Searching * SmartSearch * Advanced Search * Indexed BRCs * Entrez databases cross-referenced with StrainInfo text/html 2010-05-06T16:38:17+02:00 http://www.straininfo.net/docs/histri?rev=1273156697&do=diff What is Histri? After isolation and description, microbiological material is typically deposited in Biological Resource Centers (BRCs) to make it available for the scientific community. These BRCs distribute the material to individual researchers and other collections. Each transfer imposes a risk of contamination or human mistake, and thus of possibly confusing scientific results. In order to check the validity of strains, we need to reconstruct their exchange history ('Histri'). A histri cons… text/html 2010-05-06T16:53:51+02:00 http://www.straininfo.net/docs/histrieditor?rev=1273157631&do=diff Requirements * Java 6 Runtime Environment. The Histri Editor is launched using Java Web Start, available on most computers. If you have problems launching the application, you probably do not have a recent Java environment. Download Java here (free). text/html 2011-12-02T13:38:56+02:00 http://www.straininfo.net/docs/join?rev=1322829536&do=diff The intention of StrainInfo is to index all biological resource centers. In the initial phase, we have indexed catalogs of culture collections mainly through screen scraping (reading web pages, just as a web search engine does). Now that we have crossed the number of 50 collections, we have come up with a standard exchange format for culture collection catalogue information. This is an XML standard, which is described in detail here. Once you have done the export, all there's left is send the XM… text/html 2010-02-23T13:51:19+02:00 http://www.straininfo.net/docs/ontology?rev=1266929479&do=diff This page has moved to Microbial Common Language reference. text/html 2010-01-14T11:07:36+02:00 http://www.straininfo.net/docs/publications?rev=1263463656&do=diff About StrainInfo * Dawyndt P, Dedeurwaerdere T, Swings J. Exploring and exploiting microbiological commons: contributions of bioinformatics and intellectual property rights in sharing biological information. International Social Science Journal, 188, pp. 249-258, 2007. * Van Brabant B, Dawyndt P, De Baets B, De Vos P. A Knuckles-and-nodes approach to the integration of microbiological resource data. Lecture Notes in Computer Science, 4277, pp. 740-750, 2006. * Dawyndt P, Vancanneyt M, D… text/html 2011-12-02T13:38:56+02:00 http://www.straininfo.net/docs/searching?rev=1322829536&do=diff There are 2 main interfaces available to search on StrainInfo * SmartSearch is the easiest and recommended way to search for strains based on strain number, taxonomic name or related sequence accession number. * Advanced Search offers a more complex interface with additional search options allowing you to search based on specific criteria. text/html 2011-12-02T13:38:56+02:00 http://www.straininfo.net/docs/smartsearch?rev=1322829536&do=diff The StrainInfo 'SmartSearch' bar is prominently available on most pages. The SmartSearch field currently allows any of these inputs: * a strain number (e.g. LMG6923) * a taxonomic name (e.g. Bacillus cereus) * a sequence accession number (e.g. GN098410) text/html 2011-03-16T20:46:38+02:00 http://www.straininfo.net/docs/team?rev=1300304798&do=diff This page lists all StrainInfo team members and their individual contact details. For general inquiries, please use the general contact address. Project lead Peter Dawyndt Peter Dawyndt got the degree of M.Sc. in Mathematics in 1997 and M.Sc. in Computer Science in 1999, both from the Ghent University in Belgium. During the period 1999-2006 he worked at the Laboratory of Microbiology of the Ghent University, helping to establish a symbiosis between mathematics, computer science and the life s… text/html 2011-12-02T13:38:56+02:00 http://www.straininfo.net/docs/webservices?rev=1322829536&do=diff Web services are currently running in a private beta phase, and are not yet publicly documented or available. Contact us for web service access. In time, much of the StrainInfo query functionality and more will be available through web services. Users with specific requests for functionality are encouraged to contact us. For basic exporting of data the current web interface already allows users to export much of the data through the XML/CSV buttons below certain types of information. text/html 2010-01-14T09:17:41+02:00 http://www.straininfo.net/docs/whatisstraininfo?rev=1263457061&do=diff Using StrainInfo Searching When searching for specific strain numbers, species, genera or collections you can always use the simple search box at the top of the page. StrainInfo makes a best effort guess at what you wanted to search for and if successful it will take you straight to the relevant results. Usually if this is not the result you were looking for(say you landed on a species passport but wanted strains) you will be able to click through to more general strain search results. text/html 2010-11-29T21:25:31+02:00 http://www.straininfo.net/docs/xmlformat?rev=1291062331&do=diff Introduction This document describes the XML format used for synchronizing BRCs with StrainInfo. The format is based on a subset of the Microbial Common Language (MCL) implemented using XML. This document contains a description of how to create files for this use-case of the MCL standard. The resulting files can be validated using an XML validator and the StrainInfo catalog schema. text/html 2010-04-12T09:35:04+02:00 http://www.straininfo.net/docs/xmlimport?rev=1271057704&do=diff Please note that this procedure is currently still in beta testing phase. We hope no problems are encountered when exporting and uploading your catalog. You are welcome to give any feedback on the process. 1. Export your catalog Export your data according to the current StrainInfo XML schema for BRC catalogs. text/html 2010-04-12T09:45:02+02:00 http://www.straininfo.net/docs/xmlimportpubkey?rev=1271058302&do=diff Public key authentication for passwordless SCP operation The SCP/SFTP protocol we use to allow file uploads has the option to authenticate passwordlessly using public/private keys. This enhances security, and is especially useful in automated recurrent synchronizations, as it removes the need for interactive password prompts.