‎Provide users with better quota information (Galaxy): Added Galaxy Support Working Group, global. as mentor

← Older revision Revision as of 19:17, 1 March 2021 (3 intermediate revisions by the same user not shown)Line 97: Line 97:  * ''Skill level:'' Medium. * ''Skill level:'' Medium.  * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Solomon Shorser (solomon.shorser[AT]oicr.on.ca) * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Solomon Shorser (solomon.shorser[AT]oicr.on.ca)  +  +== Datatypes Help in Galaxy (Galaxy) ==  +  +*''Brief explanation:'' Create infrastructure for providing datatype help in Galaxy.  Includes expanding datatype definitions and updating Galaxy user interface to take advantage of it.  +*''Expected results:'' Datatype format and semantics help would be widely available when using Galaxy, including in tools that consume and produce particular datatypes, as well as server-wide help describing supported datatypes.  +*''Project Home Page URL:'' https://galaxyproject.org/  +*''Project paper reference and URL:'' Jalili, V., Afgan, E., Gu, Q., Clements, D., Blankenberg, D., Goecks, J., Taylor, J., & Nekrutenko, A. (2020). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Research, 48(W1), W395–W402. https://doi.org/10.1093/nar/gkaa434  +*''Knowledge prerequisites:''  Python and JavaScript.  Will use Vue.js components in front end.  +*''Skill level:'' Basic  +*''Mentors:'' Björn Grüning, University of Freiburg (bjoern.gruening[at]gmail.com); Dave Clements, Johns Hopkins University (clements[at]galaxyproject.org); Galaxy Support Working Group, global.  +  +== Provide users with better quota information (Galaxy) ==  +  +*''Brief explanation:'' Publish each server's quotas in a standard way; provide users with more information about what analyses and datasets are consuming their quota allocation.  +*''Expected results:'' Users will know immediately what a server's quotas are, and what items are contributing most to consuming their quota.  Users will have a clear idea of what they can expect, and what they can do to increase their available resources.  +*''Project Home Page URL:'' https://galaxyproject.org/  +*''Project paper reference and URL:'' Jalili, V., Afgan, E., Gu, Q., Clements, D., Blankenberg, D., Goecks, J., Taylor, J., & Nekrutenko, A. (2020). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Research, 48(W1), W395–W402. https://doi.org/10.1093/nar/gkaa434  +*''Knowledge prerequisites:''  Python and JavaScript.  Will use Vue.js components in front end.  +*''Skill level:'' Medium  +*''Mentors:'' Björn Grüning, University of Freiburg (bjoern.gruening[at]gmail.com); Dave Clements, Johns Hopkins University (clements[at]galaxyproject.org); Galaxy Support Working Group, global.     == Template: Project Idea Name (Project Name/Lab Name) == == Template: Project Idea Name (Project Name/Lab Name) == Clements

‎Provide users with better quota information (Galaxy): Added section

← Older revision Revision as of 02:56, 1 March 2021 (One intermediate revision by the same user not shown)Line 97: Line 97:  * ''Skill level:'' Medium. * ''Skill level:'' Medium.  * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Solomon Shorser (solomon.shorser[AT]oicr.on.ca) * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Solomon Shorser (solomon.shorser[AT]oicr.on.ca)  +  +== Datatypes Help in Galaxy (Galaxy) ==  +  +*''Brief explanation:'' Create infrastructure for providing datatype help in Galaxy.  Includes expanding datatype definitions and updating Galaxy user interface to take advantage of it.  +*''Expected results:'' Datatype format and semantics help would be widely available when using Galaxy, including in tools that consume and produce particular datatypes, as well as server-wide help describing supported datatypes.  +*''Project Home Page URL:'' https://galaxyproject.org/  +*''Project paper reference and URL:'' Jalili, V., Afgan, E., Gu, Q., Clements, D., Blankenberg, D., Goecks, J., Taylor, J., & Nekrutenko, A. (2020). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Research, 48(W1), W395–W402. https://doi.org/10.1093/nar/gkaa434  +*''Knowledge prerequisites:''  Python and JavaScript.  Will use Vue.js components in front end.  +*''Skill level:'' Basic  +*''Mentors:'' Björn Grüning, University of Freiburg (bjoern.gruening[at]gmail.com); Dave Clements, Johns Hopkins University (clements[at]galaxyproject.org)  +  +== Provide users with better quota information (Galaxy) ==  +  +*''Brief explanation:'' Publish each server's quotas in a standard way; provide users with more information about what analyses and datasets are consuming their quota allocation.  +*''Expected results:'' Users will know immediately what a server's quotas are, and what items are contributing most to consuming their quota.  Users will have a clear idea of what they can expect, and what they can do to increase their available resources.  +*''Project Home Page URL:'' https://galaxyproject.org/  +*''Project paper reference and URL:'' Jalili, V., Afgan, E., Gu, Q., Clements, D., Blankenberg, D., Goecks, J., Taylor, J., & Nekrutenko, A. (2020). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Research, 48(W1), W395–W402. https://doi.org/10.1093/nar/gkaa434  +*''Knowledge prerequisites:''  Python and JavaScript.  Will use Vue.js components in front end.  +*''Skill level:'' Medium  +*''Mentors:'' Björn Grüning, University of Freiburg (bjoern.gruening[at]gmail.com); Dave Clements, Johns Hopkins University (clements[at]galaxyproject.org)     == Template: Project Idea Name (Project Name/Lab Name) == == Template: Project Idea Name (Project Name/Lab Name) == Clements

← Older revision Revision as of 02:27, 1 March 2021 Line 37: Line 37:     == Style Guides for Biological Information Portal (WormBase / Alliance of Genome Resources)==   == Style Guides for Biological Information Portal (WormBase / Alliance of Genome Resources)==   −**''Brief explanation:'' The Alliance of Genome Resources is founded to unify access to research knowledge across different model organism systems (such as worms, flies, mouse, etc). It provides ways for published research knowledge to be categorized, aggregated and searched. The Alliance is founded by members that each specialize in a specific model organism system. They each have their own existing websites and user base (more detail on these members and their sites here: https://www.alliancegenome.org/) At the Alliance, we look to support the existing uses cases of the member sites while furthering usability and consistency. To achieve those goals, we need style guides that can be applied to the development of the Alliance website.+**''Brief explanation:'' The Alliance of Genome Resources is founded to unify access to research knowledge across different model organism systems (such as worms, flies, mouse, etc). It provides ways for published research knowledge to be categorized, aggregated, and searched. The Alliance is founded by members that each specialize in a specific model organism system. They each have their own existing websites and user base (more detail on these members and their sites here: https://www.alliancegenome.org/) At the Alliance, we look to support the existing uses cases of the member sites while furthering usability and consistency. To achieve those goals, we need style guides that can be applied to the development of the Alliance website.  **''Expected results:'' Design Prototypes and guidelines resulting from several iterations of design lifecycle. **''Expected results:'' Design Prototypes and guidelines resulting from several iterations of design lifecycle.  **''Project Home Page URL:'' https://www.alliancegenome.org/. **''Project Home Page URL:'' https://www.alliancegenome.org/. Line 46: Line 46:     == Bioinformatics with Jupyter Notebooks (WormBase)==   == Bioinformatics with Jupyter Notebooks (WormBase)==   −**''Brief explanation:'' WormBase is an informational portal for curated biological research knowledge. In additional to the website, we offer programmatic access to the data through [http://rest.wormbase.org REST API] and [ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release downloadable files]. These programatic access is intended to support bioinformatics work. We believe working examples would augment the existing documentations, making it easier for bioinformatician to access WormBase data programmatically.+**''Brief explanation:'' WormBase is an informational portal for curated biological research knowledge. In addition to the website, we offer programmatic access to the data through [http://rest.wormbase.org REST API] and [ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release downloadable files]. This programmatic access is intended to support bioinformatics work. We believe working examples would augment the existing documentation, making it easier for bioinformaticians to access WormBase data programmatically.  **''Expected results:'' A series of Jupyter Notebooks that demonstrates how WormBase data can be used in bioinformatics. **''Expected results:'' A series of Jupyter Notebooks that demonstrates how WormBase data can be used in bioinformatics.  **''Project Home Page URL:'' https://wormbase.org. **''Project Home Page URL:'' https://wormbase.org. Line 53: Line 53:  **''Skill level:'' Advanced. **''Skill level:'' Advanced.  **''Mentors:'' Sibyl Gao (sibyl@wormbase.org). **''Mentors:'' Sibyl Gao (sibyl@wormbase.org).  +  +== Authentication and Authorization Service (Alliance)==  +**''Brief explanation:'' Alliance of Genomic Resources has several services which require authentication and authorization. We would like a single service to maintain authentication and authorization across the project as the number of services increase.  +**''Expected results:'' A Service which utilizes JSON Web Tokens (JWT), Refresh Token and OAuth2 for authentication and GitHub Managed JSON files for Authorization.  +**''Project Home Page URL:'' https://www.alliancegenome.org/.  +**''Project paper reference and URL:'' [https://pubmed.ncbi.nlm.nih.gov/31796553/ The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases]  +**''Knowledge prerequisites:'' Python, Microservices.  +**''Skill level:'' Medium.  +**''Mentors:'' Adam Wright (adam.wright@wormbase.org).     == Use Galaxy to run Reactome analysis and processes on proteomics data (Reactome) == == Use Galaxy to run Reactome analysis and processes on proteomics data (Reactome) == Awright

‎Template: Updating template. Just formatting

← Older revision Revision as of 02:24, 1 March 2021 (One intermediate revision by the same user not shown)Line 56: Line 56:  == Use Galaxy to run Reactome analysis and processes on proteomics data (Reactome) == == Use Galaxy to run Reactome analysis and processes on proteomics data (Reactome) ==    −**''Brief explanation:'' 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. Galaxy is an open, web-based platform for data-intensive biomedical research, which allows users to perform, reproduce, and share complete analyses.  +*''Brief explanation:'' 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. Galaxy is an open, web-based platform for data-intensive biomedical research, which allows users to perform, reproduce, and share complete analyses.   −**''Expected results:'' There are two potential sub-projects. 1) Adding Reactome as a data resource in Galaxy, to enable Galaxy users to use Reactome reaction and pathway annotation data, and 2) Performing identifier mapping and over-representation analysis workflows from Reactome in Galaxy. Reactome [https://github.com/reactome/ Github].+*''Expected results:'' There are two potential sub-projects. 1) Adding Reactome as a data resource in Galaxy, to enable Galaxy users to use Reactome reaction and pathway annotation data, and 2) Performing identifier mapping and over-representation analysis workflows from Reactome in Galaxy. Reactome [https://github.com/reactome/ Github]. −**''Project Home Page URL:'' if there is one.+*''Project Home Page URL:'' if there is one. −**''Project paper reference and URL:'' [https://reactome.org/ reactome.org], [https://galaxyproject.org/ galaxyproject.org], [http://www.proteore.org/ ProteoRE (Proteomics Research Environment)]+*''Project paper reference and URL:'' [https://reactome.org/ reactome.org], [https://galaxyproject.org/ galaxyproject.org], [http://www.proteore.org/ ProteoRE (Proteomics Research Environment)] −**''Knowledge prerequisites:''  Galaxy, Java, web services.+*''Knowledge prerequisites:''  Galaxy, Java, web services. −**''Skill level:'' Medium.+*''Skill level:'' Medium. −**''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) and Joel Weiser (joel.weiser[AT]oicr.on.ca).+*''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) and Joel Weiser (joel.weiser[AT]oicr.on.ca).     == GraphDB API (Reactome) == == GraphDB API (Reactome) == Line 89: Line 89:  * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Solomon Shorser (solomon.shorser[AT]oicr.on.ca) * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Solomon Shorser (solomon.shorser[AT]oicr.on.ca)    −== Template ==+== Template: Project Idea Name (Project Name/Lab Name) ==    −*'''Project Idea Name (Project Name/Lab Name)'''+*''Brief explanation:'' Brief description of the idea, including any relevant links, etc.   −**''Brief explanation:'' Brief description of the idea, including any relevant links, etc.  +*''Expected results:'' describe the outcome of the project idea. −**''Expected results:'' describe the outcome of the project idea.+*''Project Home Page URL:'' if there is one. −**''Project Home Page URL:'' if there is one.+*''Project paper reference and URL:'' Is there a paper about the project this effort will be a part of? −**''Project paper reference and URL:'' Is there a paper about the project this effort will be a part of?+*''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:'' Basic, Medium or Advanced. −**''Skill level:'' Basic, Medium or Advanced.+*''Mentors:'' name + contact details of the lead mentor, name + contact details of 1 or 2 backup mentors. −**''Mentors:'' name + contact details of the lead mentor, name + contact details of 1 or 2 backup mentors.+ Clements

User account Awright was created by Scott

Scott

Creating user page for new user.

New page

I work at WormBase and Alliance as a Lead Software Developer. For WromBase I work on the Frontend Team where I mainly focus on developing the REST API. For the Alliance, I lead the Technical Planning Team and try to take on whatever work needs to be done next. I have been apart of Dr. Lincoln Stein's lab since 2012. Scott

‎Proposed project ideas for 2021

← Older revision Revision as of 18:20, 26 February 2021 (One intermediate revision by the same user not shown)Line 12: Line 12:  = Proposed project ideas for 2021 = = Proposed project ideas for 2021 =    −*'''JBrowse 2 Plugins for Additional Synteny Formats'''+== JBrowse 2 Plugins for Additional Synteny Formats==  **''Brief explanation:'' Write a new JBrowse 2 plugin to support [https://sanger-pathogens.github.io/Artemis/ACT/act-manual.html#_Toc532220687 MSPCrunch] or [http://mummer.sourceforge.net Mummer] data input **''Brief explanation:'' Write a new JBrowse 2 plugin to support [https://sanger-pathogens.github.io/Artemis/ACT/act-manual.html#_Toc532220687 MSPCrunch] or [http://mummer.sourceforge.net Mummer] data input  **''Expected results:'' a new JBrowse 2 plugin that adds support for one of the data formats listed above **''Expected results:'' a new JBrowse 2 plugin that adds support for one of the data formats listed above Line 20: Line 20:  **''Mentors:'' JBrowse development team **''Mentors:'' JBrowse development team    −*'''Interactive viewer for systems-biology variant interpretation (UI)'''+== Interactive viewer for systems-biology variant interpretation (UI)==  **''Brief explanation:'' Develop a interactive DAG linking user-specified variant to genes, cell-type expression, disease association/known cancer mutations, known drug targets. **''Brief explanation:'' Develop a interactive DAG linking user-specified variant to genes, cell-type expression, disease association/known cancer mutations, known drug targets.  **''Expected results:''  Website powered by Cytoscape.js which shows input variants as nodes, linked to different levels of system organization.   **''Expected results:''  Website powered by Cytoscape.js which shows input variants as nodes, linked to different levels of system organization.   Line 28: Line 28:  **''Mentors:'' Shraddha Pai   **''Mentors:'' Shraddha Pai            −*'''Interactive viewer for systems-biology variant interpretation (Server-side)'''+== Interactive viewer for systems-biology variant interpretation (Server-side)==  **''Brief explanation:'' Create server-side database and application for system-level annotation of variants/gene, to connect to interactive UI (e.g. selected single-cell marker datasets , known disease associations, drug targets).   **''Brief explanation:'' Create server-side database and application for system-level annotation of variants/gene, to connect to interactive UI (e.g. selected single-cell marker datasets , known disease associations, drug targets).    **''Expected results:''  Website allows users to visualize systems-level variant/gene annotation with interactive linkouts to data sources **''Expected results:''  Website allows users to visualize systems-level variant/gene annotation with interactive linkouts to data sources Line 36: Line 36:  **''Mentors:'' Shraddha Pai **''Mentors:'' Shraddha Pai    −*'''Style Guides for Biological Information Portal (WormBase / Alliance of Genome Resources)'''+== Style Guides for Biological Information Portal (WormBase / Alliance of Genome Resources)==  **''Brief explanation:'' The Alliance of Genome Resources is founded to unify access to research knowledge across different model organism systems (such as worms, flies, mouse, etc). It provides ways for published research knowledge to be categorized, aggregated and searched. The Alliance is founded by members that each specialize in a specific model organism system. They each have their own existing websites and user base (more detail on these members and their sites here: https://www.alliancegenome.org/) At the Alliance, we look to support the existing uses cases of the member sites while furthering usability and consistency. To achieve those goals, we need style guides that can be applied to the development of the Alliance website. **''Brief explanation:'' The Alliance of Genome Resources is founded to unify access to research knowledge across different model organism systems (such as worms, flies, mouse, etc). It provides ways for published research knowledge to be categorized, aggregated and searched. The Alliance is founded by members that each specialize in a specific model organism system. They each have their own existing websites and user base (more detail on these members and their sites here: https://www.alliancegenome.org/) At the Alliance, we look to support the existing uses cases of the member sites while furthering usability and consistency. To achieve those goals, we need style guides that can be applied to the development of the Alliance website.  **''Expected results:'' Design Prototypes and guidelines resulting from several iterations of design lifecycle. **''Expected results:'' Design Prototypes and guidelines resulting from several iterations of design lifecycle. Line 45: Line 45:  **''Mentors:'' Sibyl Gao (sibyl@wormbase.org). **''Mentors:'' Sibyl Gao (sibyl@wormbase.org).    −*'''Bioinformatics with Jupyter Notebooks (WormBase)'''+== Bioinformatics with Jupyter Notebooks (WormBase)==  **''Brief explanation:'' WormBase is an informational portal for curated biological research knowledge. In additional to the website, we offer programmatic access to the data through [http://rest.wormbase.org REST API] and [ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release downloadable files]. These programatic access is intended to support bioinformatics work. We believe working examples would augment the existing documentations, making it easier for bioinformatician to access WormBase data programmatically. **''Brief explanation:'' WormBase is an informational portal for curated biological research knowledge. In additional to the website, we offer programmatic access to the data through [http://rest.wormbase.org REST API] and [ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release downloadable files]. These programatic access is intended to support bioinformatics work. We believe working examples would augment the existing documentations, making it easier for bioinformatician to access WormBase data programmatically.  **''Expected results:'' A series of Jupyter Notebooks that demonstrates how WormBase data can be used in bioinformatics. **''Expected results:'' A series of Jupyter Notebooks that demonstrates how WormBase data can be used in bioinformatics. Line 53: Line 53:  **''Skill level:'' Advanced. **''Skill level:'' Advanced.  **''Mentors:'' Sibyl Gao (sibyl@wormbase.org). **''Mentors:'' Sibyl Gao (sibyl@wormbase.org).  +  +== Use Galaxy to run Reactome analysis and processes on proteomics data (Reactome) ==  +  +**''Brief explanation:'' 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. Galaxy is an open, web-based platform for data-intensive biomedical research, which allows users to perform, reproduce, and share complete analyses.  +**''Expected results:'' There are two potential sub-projects. 1) Adding Reactome as a data resource in Galaxy, to enable Galaxy users to use Reactome reaction and pathway annotation data, and 2) Performing identifier mapping and over-representation analysis workflows from Reactome in Galaxy. Reactome [https://github.com/reactome/ Github].  +**''Project Home Page URL:'' if there is one.  +**''Project paper reference and URL:'' [https://reactome.org/ reactome.org], [https://galaxyproject.org/ galaxyproject.org], [http://www.proteore.org/ ProteoRE (Proteomics Research Environment)]  +**''Knowledge prerequisites:''  Galaxy, Java, web services.  +**''Skill level:'' Medium.  +**''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) and Joel Weiser (joel.weiser[AT]oicr.on.ca).  +  +== GraphDB API (Reactome) ==  +* ''Brief explanation:'' Reactome uses both a relational database (MySQL) and a graph database (Neo4j). There is an existing API that uses the relational database, and many Reactome components use this API. To make it easier to transition these components to using the graph database, a new API with equivalent functionality needs to be created.  +* ''Expected results:'' A new Java API that interacts with the graph database, with functionality such that it could be used as a drop-in replacement for the relational database API.  +* ''Project Home Page URL:'' [https://reactome.org/ reactome.org].  +* ''Project paper reference and URL:''  +* ''Knowledge prerequisites:''  Java, MySQL. Neo4j would be good, but not necessary.  +* ''Skill level:'' Advanced.  +* ''Mentors:'' Solomon Shorser (solomon.shorser[AT]oicr.on.ca)  +  +== 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. 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  +* ''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)  +* ''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.  +* ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Solomon Shorser (solomon.shorser[AT]oicr.on.ca)     == Template == == Template == Robin.haw

‎Proposed project ideas for 2021

← Older revision Revision as of 00:36, 26 February 2021 (One intermediate revision by the same user not shown)Line 40: Line 40:  **''Expected results:'' Design Prototypes and guidelines resulting from several iterations of design lifecycle. **''Expected results:'' Design Prototypes and guidelines resulting from several iterations of design lifecycle.  **''Project Home Page URL:'' https://www.alliancegenome.org/. **''Project Home Page URL:'' https://www.alliancegenome.org/. −**''Project paper reference and URL:''The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases https://pubmed.ncbi.nlm.nih.gov/31796553/+**''Project paper reference and URL:'' [https://pubmed.ncbi.nlm.nih.gov/31796553/ The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases]  **''Knowledge prerequisites:'' Design or HCI. Knowledge of biology is preferred. **''Knowledge prerequisites:'' Design or HCI. Knowledge of biology is preferred.  **''Skill level:'' Advanced. **''Skill level:'' Advanced.  **''Mentors:'' Sibyl Gao (sibyl@wormbase.org). **''Mentors:'' Sibyl Gao (sibyl@wormbase.org).     +*'''Bioinformatics with Jupyter Notebooks (WormBase)'''  +**''Brief explanation:'' WormBase is an informational portal for curated biological research knowledge. In additional to the website, we offer programmatic access to the data through [http://rest.wormbase.org REST API] and [ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release downloadable files]. These programatic access is intended to support bioinformatics work. We believe working examples would augment the existing documentations, making it easier for bioinformatician to access WormBase data programmatically.  +**''Expected results:'' A series of Jupyter Notebooks that demonstrates how WormBase data can be used in bioinformatics.  +**''Project Home Page URL:'' https://wormbase.org.  +**''Project paper reference and URL:'' [https://pubmed.ncbi.nlm.nih.gov/31642470/ WormBase: a modern Model Organism Information Resource]  +**''Knowledge prerequisites:'' Python or R, and bioinformatics knowledge.  +**''Skill level:'' Advanced.  +**''Mentors:'' Sibyl Gao (sibyl@wormbase.org).     == Template == == Template == Sibyl

‎Proposed project ideas for 2021

← Older revision Revision as of 00:36, 26 February 2021 (2 intermediate revisions by the same user not shown)Line 36: Line 36:  **''Mentors:'' Shraddha Pai **''Mentors:'' Shraddha Pai     +*'''Style Guides for Biological Information Portal (WormBase / Alliance of Genome Resources)'''  +**''Brief explanation:'' The Alliance of Genome Resources is founded to unify access to research knowledge across different model organism systems (such as worms, flies, mouse, etc). It provides ways for published research knowledge to be categorized, aggregated and searched. The Alliance is founded by members that each specialize in a specific model organism system. They each have their own existing websites and user base (more detail on these members and their sites here: https://www.alliancegenome.org/) At the Alliance, we look to support the existing uses cases of the member sites while furthering usability and consistency. To achieve those goals, we need style guides that can be applied to the development of the Alliance website.  +**''Expected results:'' Design Prototypes and guidelines resulting from several iterations of design lifecycle.  +**''Project Home Page URL:'' https://www.alliancegenome.org/.  +**''Project paper reference and URL:'' [https://pubmed.ncbi.nlm.nih.gov/31796553/ The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases]  +**''Knowledge prerequisites:'' Design or HCI. Knowledge of biology is preferred.  +**''Skill level:'' Advanced.  +**''Mentors:'' Sibyl Gao (sibyl@wormbase.org).  +  +*'''Bioinformatics with Jupyter Notebooks (WormBase)'''  +**''Brief explanation:'' WormBase is an informational portal for curated biological research knowledge. In additional to the website, we offer programmatic access to the data through [http://rest.wormbase.org REST API] and [ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release downloadable files]. These programatic access is intended to support bioinformatics work. We believe working examples would augment the existing documentations, making it easier for bioinformatician to access WormBase data programmatically.  +**''Expected results:'' A series of Jupyter Notebooks that demonstrates how WormBase data can be used in bioinformatics.  +**''Project Home Page URL:'' https://wormbase.org.  +**''Project paper reference and URL:'' [https://pubmed.ncbi.nlm.nih.gov/31642470/ WormBase: a modern Model Organism Information Resource]  +**''Knowledge prerequisites:'' Python or R, and bioinformatics knowledge.  +**''Skill level:'' Advanced.  +**''Mentors:'' Sibyl Gao (sibyl@wormbase.org).     == Template == == Template == Sibyl

← Older revision Revision as of 03:43, 24 February 2021 Line 19: Line 19:  **''Skill level:'' Medium **''Skill level:'' Medium  **''Mentors:'' JBrowse development team **''Mentors:'' JBrowse development team  +  +*'''Interactive viewer for systems-biology variant interpretation (UI)'''  +**''Brief explanation:'' Develop a interactive DAG linking user-specified variant to genes, cell-type expression, disease association/known cancer mutations, known drug targets.  +**''Expected results:''  Website powered by Cytoscape.js which shows input variants as nodes, linked to different levels of system organization.  +**''Project Home Page URL:'' Reactome.org  +**''Knowledge prerequisites:'' JavaScript  +**''Skill level:'' Medium  +**''Mentors:'' Shraddha Pai  +  +*'''Interactive viewer for systems-biology variant interpretation (Server-side)'''  +**''Brief explanation:'' Create server-side database and application for system-level annotation of variants/gene, to connect to interactive UI (e.g. selected single-cell marker datasets , known disease associations, drug targets).  +**''Expected results:''  Website allows users to visualize systems-level variant/gene annotation with interactive linkouts to data sources  +**''Project Home Page URL:'' Reactome.org  +**''Knowledge prerequisites:'' Experience with document oriented databases (e.g. MongoDB), graphQL  +**''Skill level:'' Medium  +**''Mentors:'' Shraddha Pai  +     == Template == == Template == Shraddhapai

User account Shraddhapai was created by Scott

Scott

Creating user page for new user.

New page

Cancer is a group of related-but-different diseases with various underlying molecular networks that complicate treatment. Dr. Shraddha Pai’s research goal is to improve data-driven clinical decision-making by finding genomic and multi-omic signatures that match cancer patients to the most effective treatments with the fewest side effects. Her team uses population-scale data with multiple layers of information (e.g. transcriptomic, DNA methylation, proteomic, brain imaging, clinical), and develops algorithms and software that incorporate prior knowledge of genotype-phenotype impact and systems-level organization for predictive modeling. Dr. Pai is also interested in the role of developmental epigenetics in altering the risk of childhood- and adult-onset disease.

Prior to joining OICR’s Computational Biology Program, Dr. Pai led the development of netDx – a general-purpose patient classifier algorithm integrates heterogenous patient data into a single model to predict clinical outcome. It adapts a recommender system model similar to that used by Netflix (“find movies like this one”) to precision medicine (“find patients like non-responders”), and uses prior knowledge of cellular pathways to organize genomic data. Separately, Dr. Pai co-led the first epigenome-wide association study in neurons isolated from post-mortem brain samples in major psychosis. This study led to the identification of a novel biomarker that unifies two distinctive features of psychosis: dopaminergic increase and reduced synaptic structure.

Dr. Pai’s work and expertise in genomics and precision medicine apply to cancer as well as other diseases with genomic contribution. Scott

‎Proposed project ideas for 2021

← Older revision Revision as of 19:24, 19 February 2021 Line 12: Line 12:  = Proposed project ideas for 2021 = = Proposed project ideas for 2021 =    −''Be the first to add a project idea.''+*'''JBrowse 2 Plugins for Additional Synteny Formats'''  +**''Brief explanation:'' Write a new JBrowse 2 plugin to support [https://sanger-pathogens.github.io/Artemis/ACT/act-manual.html#_Toc532220687 MSPCrunch] or [http://mummer.sourceforge.net Mummer] data input  +**''Expected results:'' a new JBrowse 2 plugin that adds support for one of the data formats listed above  +**''Project Home Page URL:'' [https://jbrowse.org JBrowse.org]  +**''Knowledge prerequisites:''  JavaScript  +**''Skill level:'' Medium  +**''Mentors:'' JBrowse development team     == Template == == Template == RobertBuels

‎Google Summer of Code 2021 @ Open Genome Informatics

← Older revision Revision as of 18:12, 18 February 2021 Line 3: Line 3:  == Google Summer of Code 2021 @ Open Genome Informatics == == Google Summer of Code 2021 @ Open Genome Informatics ==    −'''[https://summerofcode.withgoogle.com/ Google Summer of Code]''' is a global program that offers student developers stipends to write code for various open-source software projects. We work with many open-source, free software, and technology-related groups to identify and fund projects over a three month period. Since its inception fifteen years ago, the program has brought together over 15,000 successful student participants from 109 countries, 686 open-source organizations, and has generated over 36 million lines of code. Through Google Summer of Code, accepted student applicants are paired with a mentor or mentors from the participating projects, thus gaining exposure to real-world software development scenarios and the opportunity for employment in areas related to their academic pursuits. In turn, the participating projects are able to more easily identify and bring in new developers. Best of all, more source code is created and released for the use and benefit of all. (''Excerpt from the [https://summerofcode.withgoogle.com/ Google Summer of Code website]'')+'''[https://summerofcode.withgoogle.com/ Google Summer of Code]''' is a global program that offers student developers stipends to write code for various open-source software projects. We work with many open-source, free software, and technology-related groups to identify and fund projects over a three month period. Since its inception sixteen years ago, the program has brought together over 16,000 successful student participants from 111 countries, 715 open-source organizations, and has generated over 36 million lines of code. Through Google Summer of Code, accepted student applicants are paired with a mentor or mentors from the participating projects, thus gaining exposure to real-world software development scenarios and the opportunity for employment in areas related to their academic pursuits. In turn, the participating projects are able to more easily identify and bring in new developers. Best of all, more source code is created and released for the use and benefit of all. (''Excerpt from the [https://summerofcode.withgoogle.com/ Google Summer of Code website]'')     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]. 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]. Robin.haw

‎Popular GMOD Tools

← Older revision Revision as of 22:17, 16 February 2021 (One intermediate revision by the same user not shown)Line 12: Line 12:  [http://www.linkedin.com/groups?gid=131368&trk=group-name Join other '''GMOD users''' on LinkedIn] [http://www.linkedin.com/groups?gid=131368&trk=group-name Join other '''GMOD users''' on LinkedIn]  </div> </div> −<div class="zero clear">  −[[File:MendeleyLogo-horiz.jpg|50px|right|link=http://mnd.ly/WwRe8F|GMOD group on Mendeley]]     −Keep up with GMOD papers and contribute your own in the '''[http://mnd.ly/WwRe8F GMOD group on Mendeley]'''  −</div>   <div class="compBoxHdr">[[GMOD News]][[File:RSSIcon16x16.gif|right|link={{gmod.org.url}}?title=Special%3ANewsChannel&format=rss20&limit=20&cat1=&cat2=&excat1=&wpSubmitNewsChannelParams=Create+feed|RSS feed]]<div style="float: right; padding-right: 0.5em; font-size: 80%">[[GMOD News#Adding a News Item|Add]]</div></div><rss time="1800" number="10" desc="off" title="off">http://gmod.org/wiki?title=Special%3ANewsChannel&format=rss20&limit=20&cat1=&cat2=&excat1=&wpSubmitNewsChannelParams=Create+feed</rss> <div class="compBoxHdr">[[GMOD News]][[File:RSSIcon16x16.gif|right|link={{gmod.org.url}}?title=Special%3ANewsChannel&format=rss20&limit=20&cat1=&cat2=&excat1=&wpSubmitNewsChannelParams=Create+feed|RSS feed]]<div style="float: right; padding-right: 0.5em; font-size: 80%">[[GMOD News#Adding a News Item|Add]]</div></div><rss time="1800" number="10" desc="off" title="off">http://gmod.org/wiki?title=Special%3ANewsChannel&format=rss20&limit=20&cat1=&cat2=&excat1=&wpSubmitNewsChannelParams=Create+feed</rss>  <!-- <rss max="10">http://gmod.org/mediawiki/index.php?title=Special%3ANewsChannel&format=rss20&limit=20&cat1=&cat2=&excat1=&wpSubmitNewsChannelParams=Create+feed</rss>--> <!-- <rss max="10">http://gmod.org/mediawiki/index.php?title=Special%3ANewsChannel&format=rss20&limit=20&cat1=&cat2=&excat1=&wpSubmitNewsChannelParams=Create+feed</rss>--> Line 48: Line 44:     <div class="logos"> <div class="logos"> −[[File:GitcLogo.png|250px|thumb|none|link=Cloud|GMOD in the Cloud toolset]]   [[File:GBrowseLogo.png|250px|thumb|none|link=GBrowse|GBrowse: Genome annotation viewer]] [[File:GBrowseLogo.png|250px|thumb|none|link=GBrowse|GBrowse: Genome annotation viewer]]  [[File:GalaxyLogoBigger.png|250px|thumb|none|link=Galaxy|Galaxy: Data analysis & integration]] [[File:GalaxyLogoBigger.png|250px|thumb|none|link=Galaxy|Galaxy: Data analysis & integration]] Scott

‎Preparing for GSoC 2021

← Older revision Revision as of 21:22, 16 February 2021 Line 26: Line 26:     == Preparing for GSoC 2021 == == Preparing for GSoC 2021 == −Right now it is the organization application process for GSoC - we won't know if Open Genome Informatics has been accepted as a GSOC 2021 mentoring organization until [https://developers.google.com/open-source/gsoc/timeline February 5th]. Nevertheless, it is a perfect time if students would like to talk to mentors about project ideas. If you are interested in mentoring, please check the Mentors section below, and contact the organization admin.+Right now it is the organization application process for GSoC - we won't know if Open Genome Informatics has been accepted as a GSOC 2021 mentoring organization until [https://developers.google.com/open-source/gsoc/timeline March 9th]. Nevertheless, it is a perfect time if students would like to talk to mentors about project ideas. If you are interested in mentoring, please check the Mentors section below, and contact the organization admin.     ===Students=== ===Students=== Robin.haw

← Older revision Revision as of 20:52, 16 February 2021 Line 10: Line 10:  * Serves as an informational resource on genomics database code and hardware, and provides guidance and assistance on the proper use and application of a biological database digital platform to users, team members, and researchers. * Serves as an informational resource on genomics database code and hardware, and provides guidance and assistance on the proper use and application of a biological database digital platform to users, team members, and researchers.  * Guides researchers, technicians, and others on sequence data quality assurance, storage, and extraction. * Guides researchers, technicians, and others on sequence data quality assurance, storage, and extraction. −  −[[Category:News_Items]]  Scott

← Older revision Revision as of 20:26, 16 February 2021 Line 2: Line 2:     Please see this [[Media:phoenix.pdf|job announcement]] for Phoenix Bioinformatics (home of [http://arabidopsis.org TAIR]).  Phoenix is a non-profit data publishing company. Please see this [[Media:phoenix.pdf|job announcement]] for Phoenix Bioinformatics (home of [http://arabidopsis.org TAIR]).  Phoenix is a non-profit data publishing company. −  −[[Category:News_Items]]  Scott

The Genome Informatics group and GMOD will be submitting an application for Google Summer of Code (GSoC) this year, and we are soliciting project ideas from people and groups involved in the GMOD project.

GSoC is a global program run by Google to encourage students to get real-world experience of participating in a software project; students work on a project over the summer months and receive a stipend from Google for participating. Thousands of organizations of many different sizes take part in GSoC, with the common factor being that they must produce open-source code.

Please take a look at the GSoC wiki page and think about any projects that might work well for a GSoC student, and add them to the wiki. If you are interested in being a mentor, please contact us at robin.haw@oicr.on.ca help@gmod.org.

If you have any questions--e.g. what constitutes an appropriate project; whether your idea is sufficiently GMOD-related--please feel free to email robin.haw@oicr.on.ca and help@gmod.org for advice!

Posted to the GMOD News on 2021/02/16

Created page with "link=GSoC The Genome Informatics group and GMOD will be submitting an application for [https://summerofcode.withgoogle.com/ Goo..."

New page

[[File:GoogleSummer_2016logo.jpg|272px|right|link=GSoC]]

The Genome Informatics group and GMOD will be submitting an application for [https://summerofcode.withgoogle.com/ Google Summer of Code (GSoC)] this year, and we are soliciting project ideas from people and groups involved in the GMOD project.

GSoC is a global program run by Google to encourage students to get real-world experience of participating in a software project; students work on a project over the summer months and receive a stipend from Google for participating. Thousands of organizations of many different sizes take part in GSoC, with the common factor being that they must produce open-source code.

Please take a look at the [[GSoC|GSoC wiki page]] and think about any projects that might work well for a GSoC student, and add them to the wiki. If you are interested in being a mentor, please contact us at [mailto:robin.haw@oicr.on.ca robin.haw@oicr.on.ca] [mailto:help@gmod.org help@gmod.org].

If you have any questions--e.g. what constitutes an appropriate project; whether your idea is sufficiently GMOD-related--please feel free to email [mailto:robin.haw@oicr.on.ca robin.haw@oicr.on.ca] and [mailto:help@gmod.org help@gmod.org] for advice!

{{NewsItem|2021/02/16}} Scott