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Bio

GSoD

GMOD.org recent changes - Wed, 05/06/2020 - 22:38

‎Google Season of Docs 2020 @ Open Genome Informatics

← Older revision Revision as of 02:38, 7 May 2020 (4 intermediate revisions by the same user not shown)Line 1: Line 1: −Test - to be updated+== Google Season of Docs 2020 @ Open Genome Informatics ==  +   +“Fostering open-source collaboration with technical writers” – Season of Docs  +   +Established upon the reputation of open source community programs like Google Summer of Code and Google Code-in, Google is introducing a new initiative called Season of Docs. The Open Genome Informatics has applied to participate in this year's Season of Docs.  +   +Season of Docs aims to provide open source projects with an opportunity to engage with the technical writing community and for technical writers an occasion to gain experience in contributing to open source projects.  +   +Together, we will raise community awareness of open documentation, technical writing, and how we can collectively work together to improve open source projects. Open Genome Informatics looks forward to the opportunity that Season of Docs presents and for the opportunity to bring our entire community closer together.  +   +Since 2011, the Open Genome Informatics group has served as an "umbrella organization" to a variety of bioinformatics projects, including [[Main Page|GMOD]] and its software projects -- [[JBrowse]], [[Apollo]], [[Chado]], [[Galaxy]] etc.; [http://www.informatics.jax.org/ Mouse Genome Informatics]; [https://oicr.on.ca/research-portfolio/ OICR]; [http://www.reactome.org Reactome]; [http://www.wormbase.org WormBase]; and [https://bioconda.github.io/ Bioconda].  +   +'''More information about this year's participating bioinformatics groups can be found [[GSoD_Groups | here]].'''  +   +To learn more about this year's event and how GSoD works, please refer to the [https://developers.google.com/season-of-docs FAQ].  +   +==Mailing lists, IRC, and other ways to get in touch  ==  +   +*Email: [mailto:robin.haw@oicr.on.ca robin.haw@oicr.on.ca] '''and''' [mailto:help@gmod.org help@gmod.org] -- find out more about GSoC, a specific project, or your potential mentor(s).  +*Discussion mailing lists: [http://groups.google.com/group/genome-informatics Genome Informatics Google Groups] - ask about our projects; join the community!  +*IRC channel: #genomeinformatics on Freenode.  +* Students and Mentors can email both [[User:Robin.haw|Robin]] and [[User:Scott|Scott]] to get more information about the program.  +   +==Project Ideas==  +   +Project Name: Reactome  +   +Project Description: Reactome is a free, open-source, curated and peer-reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualization, interpretation, and analysis of pathway knowledge to support basic research, genome analysis, modelling, systems biology, and education.  +   +===Project Website: https://reactome.org===  +   +====Project Idea #1 Name: Revising the Reactome User Guide====  +   +Description: The Reactome User Guide provides an introduction to Reactome, the user interfaces and the database content. Exercises are also provided to help user practice what they have learned. New functionality and improvements to the core website and software are constantly added to the User Guide. The outcome of this project is the revision of the existing User Guide, with updated and new tutorials,a set of how-to guides to support navigating the website and using the pathway visualization and analysis tools  +   +Docs Link: https://reactome.org/userguide  +   +Contacts: Robin Haw: robinhaw@gmail.com & Marc Gillepsie: gillespm@gmail.com.  +  +====Project Idea #2 Name: Updating the Reactome Curator Guide====  +   +Description: The Reactome Curator Guide contains an overview of the curatorial process as well as a step by step guide for annotating Reactome pathways. The curator guide takes new curators through the process of project design, entry, review, and release. Each one of these steps requires that the curator is familiar with the Reactome data model, software entry tools, process pipeline, and project management. In this sense, the curator guide serves as a compendium of learned lessons, curator philosophy, and a step-by-step process blueprint. The outcome of this project is the complete revision of the current guide to reflect new data entry tools, update the current glossary of terms to accommodate changes to data model, and create short tutorials that can be used to reinforce each learning step.  +   +Contacts: Marc Gillepsie gillespm@gmail.com and Robin Haw: robinhaw@gmail.com Robin.haw
Categories: Bio

GSoD

GMOD.org recent changes - Fri, 05/01/2020 - 15:33

Created page with "Test - to be updated "

New page

Test - to be updated Robin.haw
Categories: Bio

AGR GFF

AGR GFF uploads - Tue, 04/28/2020 - 23:35
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Categories: Bio

AGR VCF: 1588120337

AGR VCF uploads - Tue, 04/28/2020 - 20:35
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Categories: Bio

AGR GFF: 1588120381

AGR GFF uploads - Tue, 04/28/2020 - 20:35
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Categories: Bio

AGR GFF: 1588113577

AGR GFF uploads - Tue, 04/28/2020 - 19:05
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Categories: Bio

gmod.org is DOWN, 1586527681

GMOD.org status - Fri, 04/10/2020 - 10:35
Categories: Bio

gmod.org is DOWN, 1586520481

GMOD.org status - Fri, 04/10/2020 - 08:35
Categories: Bio

JBrowse Configuration Guide

GMOD.org recent changes - Tue, 03/24/2020 - 16:46

← Older revision Revision as of 20:46, 24 March 2020 Line 3,492: Line 3,492:         //page.on('console', msg => console.log('PAGE LOG:', msg.text()));        //page.on('console', msg => console.log('PAGE LOG:', msg.text()));         await page.setViewport({        await page.setViewport({ −         width:argv[4]||1000,+         width:+argv[4]||1000, −         height:argv[5]||600,+         height:+argv[5]||600,           deviceScaleFactor:argv[6]||2          deviceScaleFactor:argv[6]||2         });        }); Colin Diesh
Categories: Bio

GSOC Project Ideas 2020

GMOD.org recent changes - Wed, 03/18/2020 - 22:14

‎Community access portal to Reactome Archive (Reactome)

← Older revision Revision as of 02:14, 19 March 2020 (2 intermediate revisions by the same user not shown)Line 98: Line 98:  * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Joel Weiser (joel.weiser[AT]oicr.on.ca) * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Joel Weiser (joel.weiser[AT]oicr.on.ca)    −==Creating NCBI GeneRIFs and other data exports (Reactome)==+==Community access portal to Reactome Archive (Reactome)== −**''Brief explanation:'' Reactome already links to NCBI Gene, Protein, and OMIM web pages. NCBI has a mechanism that third party collaborators can use to add information to RefSeq and NCBI Gene using the GeneRIF system. We will create an export tool to contribute summary sentences detailing pathways, reactions and complexes that the gene participates in, including the gene’s functional role, with PubMed and Reactome stable identifiers that will allow linkage back to the relevant Reactome pathway and curated literature. Other data exports are under consideration.+*''Brief explanation:'' Reactome generates new pathway and other annotation data on a quarterly basis. With each new release, the preceding data set is archived to an AWS S3 bucket. As part of our data sharing policy, we would like to develop web interface to allow users to request specific versions of archived data and to make it available to download.   −**''Expected results:'' Scripts to export data, QA steps, export data files.+*''Expected results:'' Web interface for users to request data and download via a shareable link that either expires within a certain timeframe or after data is downloaded.  * ''Project Home Page URL:'' [https://reactome.org. reactome.org]. * ''Project Home Page URL:'' [https://reactome.org. reactome.org]. −* ''Knowledge prerequisites:'' Java, MySQL and/or Neo4j+* ''Knowledge prerequisites:'' Java, AWS, Joomla  * ''Skill level:'' Medium. * ''Skill level:'' Medium.  * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Joel Weiser (joel.weiser[AT]oicr.on.ca) * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Joel Weiser (joel.weiser[AT]oicr.on.ca) −  −Community access portal to Reactome Archive.  −      == Community data submission (WormBase) == == Community data submission (WormBase) == Robin.haw
Categories: Bio

GSOC Project Ideas 2020

GMOD.org recent changes - Wed, 03/18/2020 - 22:14

‎Community access portal to Reactome Archive (Reactome)

← Older revision Revision as of 02:14, 19 March 2020 (5 intermediate revisions by the same user not shown)Line 71: Line 71:  * ''Knowledge prerequisites:''  Java, MySQL, (optional) Neo4j, AWS * ''Knowledge prerequisites:''  Java, MySQL, (optional) Neo4j, AWS  * ''Skill level:'' Medium * ''Skill level:'' Medium −* ''Mentors:'' Justin Cook (justin.cook[AT]oicr.on.ca)+* ''Mentors:'' Justin Cook (justin.cook[AT]oicr.on.ca) and Robin Haw (robin.haw[AT]oicr.on.ca)     == GraphDB API (Reactome) == == GraphDB API (Reactome) == Line 80: Line 80:  * ''Knowledge prerequisites:''  Java, MySQL. Neo4j would be good, but not necessary. * ''Knowledge prerequisites:''  Java, MySQL. Neo4j would be good, but not necessary.  * ''Skill level:'' Advanced. * ''Skill level:'' Advanced. −* ''Mentors:'' Solomon Shorser (solomon.shorser[AT]oicr.on.ca).+* ''Mentors:'' Solomon Shorser (solomon.shorser[AT]oicr.on.ca)     == GraphQL interface for querying Reactome data (Reactome) == == GraphQL interface for querying Reactome data (Reactome) == Line 95: Line 95:  * ''Project Home Page URL:'' [https://reactome.org. reactome.org]. * ''Project Home Page URL:'' [https://reactome.org. reactome.org].  * ''Knowledge prerequisites:'' Java, MySQL and/or Neo4j, creating visuals for statistical data (preferred but not required) * ''Knowledge prerequisites:'' Java, MySQL and/or Neo4j, creating visuals for statistical data (preferred but not required)  +* ''Skill level:'' Medium.  +* ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Joel Weiser (joel.weiser[AT]oicr.on.ca)  +  +==Community access portal to Reactome Archive (Reactome)==  +*''Brief explanation:'' Reactome generates new pathway and other annotation data on a quarterly basis. With each new release, the preceding data set is archived to an AWS S3 bucket. As part of our data sharing policy, we would like to develop web interface to allow users to request specific versions of archived data and to make it available to download.   +*''Expected results:'' Web interface for users to request data and download via a shareable link that either expires within a certain timeframe or after data is downloaded.  +* ''Project Home Page URL:'' [https://reactome.org. reactome.org].  +* ''Knowledge prerequisites:'' Java, AWS, Joomla  * ''Skill level:'' Medium. * ''Skill level:'' Medium.  * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Joel Weiser (joel.weiser[AT]oicr.on.ca) * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Joel Weiser (joel.weiser[AT]oicr.on.ca) Robin.haw
Categories: Bio

GSOC Project Ideas 2020

GMOD.org recent changes - Wed, 03/18/2020 - 09:46

‎Proposed project ideas for 2020

← Older revision Revision as of 13:46, 18 March 2020 (2 intermediate revisions by the same user not shown)Line 71: Line 71:  * ''Knowledge prerequisites:''  Java, MySQL, (optional) Neo4j, AWS * ''Knowledge prerequisites:''  Java, MySQL, (optional) Neo4j, AWS  * ''Skill level:'' Medium * ''Skill level:'' Medium −* ''Mentors:'' Justin Cook (justin.cook[AT]oicr.on.ca)+* ''Mentors:'' Justin Cook (justin.cook[AT]oicr.on.ca) and Robin Haw (robin.haw[AT]oicr.on.ca)     == GraphDB API (Reactome) == == GraphDB API (Reactome) == Line 80: Line 80:  * ''Knowledge prerequisites:''  Java, MySQL. Neo4j would be good, but not necessary. * ''Knowledge prerequisites:''  Java, MySQL. Neo4j would be good, but not necessary.  * ''Skill level:'' Advanced. * ''Skill level:'' Advanced. −* ''Mentors:'' Solomon Shorser (solomon.shorser[AT]oicr.on.ca).+* ''Mentors:'' Solomon Shorser (solomon.shorser[AT]oicr.on.ca)     == GraphQL interface for querying Reactome data (Reactome) == == GraphQL interface for querying Reactome data (Reactome) == Line 97: Line 97:  * ''Skill level:'' Medium. * ''Skill level:'' Medium.  * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Joel Weiser (joel.weiser[AT]oicr.on.ca) * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Joel Weiser (joel.weiser[AT]oicr.on.ca)  +  +==Creating NCBI GeneRIFs and other data exports (Reactome)==  +**''Brief explanation:'' Reactome already links to NCBI Gene, Protein, and OMIM web pages. NCBI has a mechanism that third party collaborators can use to add information to RefSeq and NCBI Gene using the GeneRIF system. We will create an export tool to contribute summary sentences detailing pathways, reactions and complexes that the gene participates in, including the gene’s functional role, with PubMed and Reactome stable identifiers that will allow linkage back to the relevant Reactome pathway and curated literature. Other data exports are under consideration.  +**''Expected results:'' Scripts to export data, QA steps, export data files.  +* ''Project Home Page URL:'' [https://reactome.org. reactome.org].  +* ''Knowledge prerequisites:'' Java, MySQL and/or Neo4j  +* ''Skill level:'' Medium.  +* ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Joel Weiser (joel.weiser[AT]oicr.on.ca)  +  +Community access portal to Reactome Archive.  +     == Community data submission (WormBase) == == Community data submission (WormBase) == Robin.haw
Categories: Bio

GSOC Project Ideas 2020

GMOD.org recent changes - Mon, 03/16/2020 - 21:56

‎JBrowse 2 - Phylogenetic tree viewer

← Older revision Revision as of 01:56, 17 March 2020 (2 intermediate revisions by the same user not shown)Line 156: Line 156:  * ''Expected results:'' A beautiful and fast tree viewer in JBrowse 2, written using React and mobx-state-tree. * ''Expected results:'' A beautiful and fast tree viewer in JBrowse 2, written using React and mobx-state-tree.  * ''Project Home Page URL:'' https://jbrowse.org   * ''Project Home Page URL:'' https://jbrowse.org    +* ''Project Chat:'' https://gitter.im/GMOD/jbrowse  * ''Knowledge prerequisites:'' JavaScript, React * ''Knowledge prerequisites:'' JavaScript, React  * ''Skill level:'' Advanced * ''Skill level:'' Advanced Line 164: Line 165:  * ''Expected results:'' New features in JBrowse 2 for predicting and visualizing variant effects * ''Expected results:'' New features in JBrowse 2 for predicting and visualizing variant effects  * ''Project Home Page URL:'' https://jbrowse.org   * ''Project Home Page URL:'' https://jbrowse.org    +* ''Project Chat:'' https://gitter.im/GMOD/jbrowse  * ''Knowledge prerequisites:'' JavaScript, React * ''Knowledge prerequisites:'' JavaScript, React  * ''Skill level:'' Medium * ''Skill level:'' Medium Line 172: Line 174:  * ''Expected results:'' New features in JBrowse 2 for predicting and visualizing variant effects * ''Expected results:'' New features in JBrowse 2 for predicting and visualizing variant effects  * ''Project Home Page URL:'' https://jbrowse.org   * ''Project Home Page URL:'' https://jbrowse.org    +* ''Project Chat:'' https://gitter.im/GMOD/jbrowse  * ''Knowledge prerequisites:'' JavaScript, React * ''Knowledge prerequisites:'' JavaScript, React  * ''Skill level:'' Advanced * ''Skill level:'' Advanced  * ''Mentors:'' JBrowse Development Team (Robert Buels, Colin Diesh, Garrett Stevens, or Peter Xie) * ''Mentors:'' JBrowse Development Team (Robert Buels, Colin Diesh, Garrett Stevens, or Peter Xie) Colin Diesh
Categories: Bio

GSOC Project Ideas 2020

GMOD.org recent changes - Fri, 03/13/2020 - 18:49

‎Automated Bioinformatics Help in Galaxy: Added mentors

← Older revision Revision as of 22:49, 13 March 2020 Line 40: Line 40:  * ''Knowledge prerequisites:''  programming language(s) to be used, plus any other particular computer science skills needed. * ''Knowledge prerequisites:''  programming language(s) to be used, plus any other particular computer science skills needed.  * ''Skill level:'' Medium. * ''Skill level:'' Medium. −* ''Mentors:''+* ''Mentors:'' [https://galaxyproject.org/people/sergey/ Sergey Golitsynskiy], [[User:Clements|Dave Clements]]     == Use Galaxy to run Reactome analysis and processes on genomic data (Reactome) == == Use Galaxy to run Reactome analysis and processes on genomic data (Reactome) == Clements
Categories: Bio

User:Jmill3082

GMOD.org recent changes - Thu, 03/12/2020 - 20:06

Creating user page for new user.

New page

Graduate student at Johns Hopkins University.
NSF Graduate Research Fellow.
Working in the Gordus lab in the Biology Department.
I am interested in how behaviors that are structured over long timescales are coded genetically and at the cellular/circuit level in the brain.
I am using the orb-weaving spider Uloborus diversus to study the web-building behavior.
Currently, I am working on annotating the genome of this organism. Scott
Categories: Bio

User:Jmill3082

GMOD.org recent changes - Thu, 03/12/2020 - 20:06

User account Jmill3082 was created by Scott

Scott
Categories: Bio

User:Garrett

GMOD.org recent changes - Thu, 03/12/2020 - 19:45

Creating user page for new user.

New page

Garrett has been a core developer for JBrowse since 2018, working for Ian Holmes at UC Berkeley. He graduated from the University of Utah with a BS in Physics in 2015 and Brandeis University with an MS in Bioinformatics in 2019. He currently lives near Salt Lake City, UT, but has also lived in Massachusetts and Japan. Scott
Categories: Bio

User:Garrett

GMOD.org recent changes - Thu, 03/12/2020 - 19:45

User account Garrett was created by Scott

Scott
Categories: Bio

GSOC Project Ideas 2020

GMOD.org recent changes - Wed, 03/11/2020 - 15:45

‎Statistics consolidation/display of release data (Reactome)

← Older revision Revision as of 19:45, 11 March 2020 Line 90: Line 90:  * ''Mentors:'' Joel Weiser (joel.weiser[AT]oicr.on.ca) * ''Mentors:'' Joel Weiser (joel.weiser[AT]oicr.on.ca)    −== Statistics consolidation/display of release data (Reactome) ==+== Centralized dashboard or metrics system (Reactome) == −* ''Brief explanation:'' Reactome has both manual and automated statistical tracking of its quarterly release data.  This project would seek to fully automate and consolidate the quantification of release data measurement for metrics such as the number of pathways, reactions, distinct proteins (with and without UniProt isoforms), complexes, small molecules, drugs/therapeutics, literature references, etc. for human (curated) and non-human (electronically inferred) species and stratified for normal and disease biology+* ''Brief explanation:'' Reactome has both manual and automated statistical tracking of its quarterly release data.  This project would seek to fully automate and consolidate the quantification of release data measurement for metrics such as the number of pathways, reactions, distinct proteins (with and without UniProt isoforms), complexes, small molecules, drugs/therapeutics, literature references, etc. for human (curated) and non-human (electronically inferred) species and stratified for normal and disease biology. a centralized dashboard would be useful by the team for discussing metrics externally and community outreach.  * ''Expected results:'' A program which will produce a standardized report of statistics for a Reactome release database with aesthetic visuals * ''Expected results:'' A program which will produce a standardized report of statistics for a Reactome release database with aesthetic visuals  * ''Project Home Page URL:'' [https://reactome.org. reactome.org]. * ''Project Home Page URL:'' [https://reactome.org. reactome.org].  * ''Knowledge prerequisites:'' Java, MySQL and/or Neo4j, creating visuals for statistical data (preferred but not required) * ''Knowledge prerequisites:'' Java, MySQL and/or Neo4j, creating visuals for statistical data (preferred but not required)  * ''Skill level:'' Medium. * ''Skill level:'' Medium. −* ''Mentors:'' Joel Weiser (joel.weiser[AT]oicr.on.ca)+* ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Joel Weiser (joel.weiser[AT]oicr.on.ca)     == Community data submission (WormBase) == == Community data submission (WormBase) == Robin.haw
Categories: Bio

gmod.org is DOWN, 1583770081

GMOD.org status - Mon, 03/09/2020 - 12:35
Categories: Bio

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