Bio

Prospecting for Proposals for GSoC 2020

GMOD News - Tue, 02/04/2020 - 01:41
GoogleSummer 2016logo.jpg

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 2020/02/03
Categories: Bio

News/Prospecting for Proposals for GSoC 2020

GMOD.org recent changes - Tue, 02/04/2020 - 01:41

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!

[[Category:GSOC]]
[[Category:GSoC]]
[[Category:News_Items]] Robin.haw
Categories: Bio

GSOC Project Ideas 2020

GMOD.org recent changes - Mon, 02/03/2020 - 17:25

‎GraphQL over Microservice Architecture (WormBase / Alliance of Genome Resources)

← Older revision Revision as of 22:25, 3 February 2020 (12 intermediate revisions by the same user not shown)Line 61: Line 61:  **''Skill level:'' Medium. **''Skill level:'' Medium.  **''Mentors:''  Joel Weiser (joel.weiser[AT]oicr.on.ca). **''Mentors:''  Joel Weiser (joel.weiser[AT]oicr.on.ca).  +  +== Community data submission (WormBase) ==  +* ''Brief explanation:'' WormBase is a comprehensive research knowledgebase on the biology of nematodes. Our database is built by extracting and standardizing information from published literature, which is time consuming and low throughput. Hence, we would like to encourage our users, who also derive the knowledge originally, to submit their findings through our website. This would speed up the integration of knowledge in our database and diversify our data sources.  +* ''Expected results:'' Website frontend components and backend mechanisms that allow inline data submission from users, realtime update of the website, notification and mechanism for review and integrate the data into WormBase database.  +* ''Project Home Page URL:'' https://wormbase.org  +* ''Project paper reference and URL:'' https://academic.oup.com/nar/article/48/D1/D762/5603222  +* ''Knowledge prerequisites:'' JavaScript, experience building cloud native solution preferred.  +* ''Skill level:'' Advanced  +* ''Mentors:'' Todd Harris (todd[AT]wormbase.org), Sibyl Gao (sibyl[AT]wormbase.org).  +  +== Data Table functionality and performance (WormBase) ==  +* ''Brief explanation'': WormBase is a comprehensive research knowledgebase on the biology of nematodes. Biologists access our vast information through a web port which often provides information in many tables. Here is an example page of a well-studied gene in C. elegans, dat-6, https://wormbase.org/species/c_elegans/gene/WBGene00000912#01347b--10. These tables where developed years ago based on HTML and jQuery, with certain features depending on Flash. Their limitations and usability issues are more pronounced now. Hence, we are looking for a new implementation of these tables with React, which is used in many parts of the site.  +* ''Expected results:'' A generic and customizable table component in React for displaying WormBase data, with the ability to search, filter, sort, paginate, and export all or parts of the table.  +* ''Project Home Page URL:'' https://wormbase.org  +* ''Project paper reference and URL:'' https://academic.oup.com/nar/article/48/D1/D762/5603222  +* ''Knowledge prerequisites:'' JavaScript, CSS, React.  +* ''Skill level:'' Medium  +* ''Mentors:'' Sibyl Gao (sibyl[AT]wormbase.org).  +  +== GraphQL over Microservice Architecture (WormBase / Alliance of Genome Resources) ==  +* ''Brief explanation:'' As a data resource, we seek to make our data accessible through web APIs. [https://graphql.org/ GraphQL], a new web API specification, provides programmatic access users a powerful way to retrieve our data. However, a single monolithic GraphQL service will be difficult for us to manage due to heterogeneous data types and geographically distributed teams. We would like to allow different teams (each organized around a knowledge domain) to independently develop and deploy GraphQL services, and combine them into a single GraphQL schema and API endpoint that can be queried easily cross-domain. [https://www.apollographql.com/docs/apollo-server/federation/introduction/ Apollo Federation] seems to be what we need, and we’d like to assess its viability as a solution to our problem.  +* ''Expected results:'' Prototype for expressing multiple independently developed and deployed GraphQL services as a single graph using Apollo Federation.  +* ''Project Home Page URL:'' https://wormbase.org  +* ''Project paper reference and URL:'' https://academic.oup.com/nar/article/48/D1/D762/5603222  +* ''Knowledge prerequisites:'' JavaScript, microservice architecture.  +* ''Skill level:'' Advanced  +* ''Mentors:'' Sibyl Gao (sibyl[AT]wormbase.org).  +  +== Single Sign On (WormBase) ==  +* ''Brief explanation:'' WormBase consists of an ecosystem of tools, some of which we developed ourselves, others we adopted from the community. Several of these tools require a user to be signed in, giving rise to multiple implementations of authentication and unnecessary difficulties in user experience.  +* ''Expected results:'' That users only need to sign-in once on WormBase. We would like to have a centrally managed authentication service that allows individual services to manage their own authorization. And we would need a migration plan for the tools that currently manages its own authentication.  +* ''Project Home Page URL:'' https://wormbase.org  +* ''Project paper reference and URL:'' https://academic.oup.com/nar/article/48/D1/D762/5603222  +* ''Knowledge prerequisites:'' Authentication and Authorization (JWT, OAuth2).  +* ''Skill level:'' Advanced  +* ''Mentors:'' Sibyl Gao (sibyl[AT]wormbase.org).  +  +== Faster Autocompletion (WormBase Name Service) ==  +* ''Brief explanation:'' As a biological knowledge base, WormBase uses unique stable identifiers to biological entities described in scientific publications (such a s gene or a variation, etc). The tasks to create an identifier and to lookup information associated with it (such as its common name and metadata) is handled by a tool, called the Name Service. The performance of the Name Service is currently hindered by the slowness of the autocompletion, which is performed directly on the database that is not optimized for this type of query. We are looking to implement an autocomplete solution using a search engine, such as Elasticsearch.  +* ''Expected results:'' A faster REST API to retrieve autocomplete suggestions from, and the necessary workflow to ensure the search engine highly available and up-to-date with the database.  +* ''Project Home Page URL:'' https://wormbase.org  +* ''Project paper reference and URL:'' https://academic.oup.com/nar/article/48/D1/D762/5603222  +* ''Knowledge prerequisites:'' Elasticsearch, Clojure (or another LISP)  +* ''Skill level:'' Medium  +* ''Mentors:'' Sibyl Gao (sibyl[AT]wormbase.org).  +  +== Word and sentence completion for curatorial remarks (WormBase Name Service) ==  +* ''Brief explanation:'' As a biological research knowledgebase, WormBase aggregates and standardizes experimental findings reported in research literature. This work is often done with the help of our curators, who, in addition to filling in standardized forms, write free-text remarks providing additional context. We would like a word and sentence completion tool that reduces the amount of repetitive typing that a curator does, without hindering their ability to compose original content if they so choose.  +* ''Expected results:'' An performant in-browser word and sentence completion tool, similar to [https://research.google/pubs/pub48231/ Gmail Smart Compose], that suggest words based on previously composed content, available through an API.  +* ''Project Home Page URL:'' https://wormbase.org  +* ''Project paper reference and URL:'' https://academic.oup.com/nar/article/48/D1/D762/5603222  +* ''Knowledge prerequisites:'' NLP, JavaScript  +* ''Skill level:'' Advanced  +* ''Mentors:'' Sibyl Gao (sibyl[AT]wormbase.org). Sibyl
Categories: Bio

GSOC Project Ideas 2020

GMOD.org recent changes - Mon, 02/03/2020 - 17:05

‎Data Table functionality and performance (WormBase)

← Older revision Revision as of 22:05, 3 February 2020 (4 intermediate revisions by the same user not shown)Line 61: Line 61:  **''Skill level:'' Medium. **''Skill level:'' Medium.  **''Mentors:''  Joel Weiser (joel.weiser[AT]oicr.on.ca). **''Mentors:''  Joel Weiser (joel.weiser[AT]oicr.on.ca).  +  +== Community data submission (WormBase) ==  +* ''Brief explanation:'' WormBase is a comprehensive research knowledgebase on the biology of nematodes. Our database is built by extracting and standardizing information from published literature, which is time consuming and low throughput. Hence, we would like to encourage our users, who also derive the knowledge originally, to submit their findings through our website. This would speed up the integration of knowledge in our database and diversify our data sources.  +* ''Expected results:'' Website frontend components and backend mechanisms that allow inline data submission from users, realtime update of the website, notification and mechanism for review and integrate the data into WormBase database.  +* ''Project Home Page URL:'' https://wormbase.org  +* ''Project paper reference and URL:'' https://academic.oup.com/nar/article/48/D1/D762/5603222  +* ''Knowledge prerequisites:'' JavaScript, experience building cloud native solution preferred.  +* ''Skill level:'' Advanced  +* ''Mentors:'' Todd Harris (todd[AT]wormbase.org), Sibyl Gao (sibyl[AT]wormbase.org).  +  +== Data Table functionality and performance (WormBase) ==  +* ''Brief explanation'': WormBase is a comprehensive research knowledgebase on the biology of nematodes. Biologists access our vast information through a web port which often provides information in many tables. Here is an example page of a well-studied gene in C. elegans, dat-6, https://wormbase.org/species/c_elegans/gene/WBGene00000912#01347b--10. These tables where developed years ago based on HTML and jQuery, with certain features depending on Flash. Their limitations and usability issues are more pronounced now. Hence, we are looking for a new implementation of these tables with React, which is used in many parts of the site.  +* ''Expected results:'' A generic and customizable table component in React for displaying WormBase data, with the ability to search, filter, sort, paginate, and export all or parts of the table.  +* ''Project Home Page URL:'' https://wormbase.org  +* ''Project paper reference and URL:'' https://academic.oup.com/nar/article/48/D1/D762/5603222  +* ''Knowledge prerequisites:'' JavaScript, CSS, React.  +* ''Skill level:'' Medium  +* ''Mentors:'' Sibyl Gao (sibyl[AT]wormbase.org).  +  +== GraphQL over Microservice Architecture (WormBase / Alliance of Genome Resources) ==  +  +== Single Sign On (WormBase) ==  +  +== Faster Autocompletion (WormBase Name Service) ==  +  +== Word and sentence completion for curatorial remarks (WormBase Name Service) == Sibyl
Categories: Bio

User:Miharimamy

GMOD.org recent changes - Mon, 02/03/2020 - 16:28

Creating user page for new user.

New page

Microbiologist and fullstack developer, my field of research evolves around knowledge representation and data mining applied to bioinformatics and health informatics.
I got a master degree in biotechnology and a bachelor degree in computer science mainly because the bioinformatic major was not open yet at the time. So I decided to mix in my love of biology with my programming skills through a PhD in Genomics and Bioinformatics.
To brush up my skills, I got a year-long experience in a tech company as a fullstack developer in JavaScript and get the good practices for application industry standards.
I like sharing and collaborating with passionate people like myself about various subjects : art, math, physics, biology and obviously computer science. Scott
Categories: Bio

User:Miharimamy

GMOD.org recent changes - Mon, 02/03/2020 - 16:28

User account Miharimamy was created by Scott

Scott
Categories: Bio

User:Sibyl

GMOD.org recent changes - Mon, 02/03/2020 - 16:13

Creating user page for new user.

New page

Software Developer @ WormBase. I completed my undergraduate in Microbiology and Computer Science at University of British Columbia. My expertise is in full-stack web development, cloud computing (AWS) and exploratory/visual data analysis. I am a user experience enthusiast, always seeking ways to make our product better by trying to understand our users more. Scott
Categories: Bio

User:Sibyl

GMOD.org recent changes - Mon, 02/03/2020 - 16:13

User account Sibyl was created by Scott

Scott
Categories: Bio

GSOC Project Ideas 2020

GMOD.org recent changes - Wed, 01/29/2020 - 11:21

← Older revision Revision as of 16:21, 29 January 2020 Line 60: Line 60:  **''Knowledge prerequisites:''  R Programming Language, Neo4J. **''Knowledge prerequisites:''  R Programming Language, Neo4J.  **''Skill level:'' Medium. **''Skill level:'' Medium. −**''Mentors:''  Joel Weiser (joel.weiser[AT]oicr.on.ca) and Antonio Fabregat (fabregat[AT]ebi.ac.uk).+**''Mentors:''  Joel Weiser (joel.weiser[AT]oicr.on.ca). Jweiser
Categories: Bio

GSoC

GMOD.org recent changes - Tue, 01/28/2020 - 15:58

‎Preparing for GSoC 2020

← Older revision Revision as of 20:58, 28 January 2020 (3 intermediate revisions by the same user not shown)Line 1: Line 1:  [[File:GoogleSummer_2016logo.jpg|373px|right|link=GSoC]] [[File:GoogleSummer_2016logo.jpg|373px|right|link=GSoC]]    −== Google Summer of Code 2019 @ Open Genome Informatics ==+== Google Summer of Code 2020 @ 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 in 2005, the program has brought together over 14,000 successful student participants from 118 countries, 651 open source organizations, and over 35 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 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]'')     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]. Line 18: Line 18:  * Students and Mentors can email both [[User:Robin.haw|Robin]] and [[User:Scott|Scott]] to get more information about the program. * Students and Mentors can email both [[User:Robin.haw|Robin]] and [[User:Scott|Scott]] to get more information about the program.    −== [[GSOC_Project_Ideas_2019 | Project Ideas]] ==+== [[GSOC_Project_Ideas_2020 | Project Ideas]] ==    −'''Got an idea for a GSOC project? [[GSOC_Project_Ideas_2019 |Add it here]].'''  Ideas will be included in the proposal we send to GSOC, and great ideas make for a great proposal, so please add yours now.+'''Got an idea for a GSOC project? [[GSOC_Project_Ideas_2020 |Add it here]].'''  Ideas will be included in the proposal we send to GSOC, and great ideas make for a great proposal, so please add yours now.          −These projects can use a broad set of skills, technologies, and domains, such as GUIs, database integration, and algorithms. Students are also encouraged to propose their own ideas related to our projects. If you have strong computer skills and have an interest in biology or bioinformatics, you should definitely apply! '''Do not hesitate to propose your own project idea: some of the best applications we see are by students that go this route.''' As long as it is relevant to one of our projects, we will give it serious consideration. Creativity and self-motivation are great traits for open source programmers.+These projects can use a broad set of skills, technologies, and domains, such as GUIs, database integration, and algorithms. Students are also encouraged to propose their own ideas related to our projects. If you have strong computer skills and have an interest in biology or bioinformatics, you should definitely apply! <br>  +'''Do not hesitate to propose your own project idea: some of the best applications we see are by students that go this route.''' As long as it is relevant to one of our projects, we will give it serious consideration. Creativity and self-motivation are great traits for open-source programmers.    − +== Preparing for GSoC 2020 == −== Preparing for GSoC 2019 ==+Right now it is the organization application process for GSoC - we won't know if Open Genome Informatics has been accepted as a GSOC 2020 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 2019 mentoring organization until [https://developers.google.com/open-source/gsoc/timeline February 6th]. 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=== Line 32: Line 32:     ===Mentors=== ===Mentors=== −We encourage mentors and mentoring organizations to think about new projects year round! If you'd like help with your ideas page or your separate mentoring org application, please feel to contact the organization admins. Links to [[GSOC_Mentoring_Guide | advice about mentoring and other resources]] are available.+We encourage mentors and mentoring organizations to think about new projects year-round! If you'd like help with your ideas page or your separate mentoring org application, please feel to contact the organization admins. Links to [[GSOC_Mentoring_Guide | advice about mentoring and other resources]] are available.     [[Category:Galaxy]] [[Category:Galaxy]] Robin.haw
Categories: Bio

GSOC Project Ideas 2020

GMOD.org recent changes - Tue, 01/28/2020 - 15:54

Created page with "'''Got an idea for GSOC 2020?''' Then please post it. You can either # Add it here, by directly editing this page. Just copy, paste and update the #Template|tem..."

New page

'''Got an idea for [[GSoC|GSOC 2020]]?'''

Then please post it. You can either

# Add it here, by directly editing this page. Just copy, paste and update the [[#Template|template]] below. This requires that you have or create a GMOD.org login.

Projects can use a broad set of skills, technologies, and domains, such as GUIs, database integration and algorithms.

Students are also encouraged to propose their own ideas related to our projects. If you have strong computer skills and have an interest in biology or bioinformatics, you should definitely apply! Do not hesitate to propose your own project idea: some of the best applications we see are by students that go this route. As long as it is relevant to one of our projects, we will give it serious consideration. Creativity and self-motivation are great traits for open-source programmers.


= Proposed project ideas for 2020 =

''Be the first to add a project idea.''

== Template ==

*'''Project Idea Name (Project Name/Lab Name)'''
**''Brief explanation:'' Brief description of the idea, including any relevant links, etc.
**''Expected results:'' describe the outcome of the project idea.
**''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?
**''Knowledge prerequisites:'' programming language(s) to be used, plus any other particular computer science skills needed.
**''Skill level:'' Basic, Medium or Advanced.
**''Mentors:'' name + contact details of the lead mentor, name + contact details of 1 or 2 backup mentors.


== Automated Bioinformatics Help in Galaxy ==

*''Brief explanation:''
** [https://galaxyproject.org/ Galaxy] users often encounter errors when trying to run a bioinformatics analysis. These errors may be user or data errors (e.g. misformatted dataset) or errors due to underlying computing hardware (e.g. disk is full). Helping users and Galaxy support staff determine the kind of error they encountered would be useful because a user can likely address the first type of error, while the second type requires expert invention.
** This project will improve Galaxy’s error system by using heuristics or machine learning to identify common types of user/data errors and make suggestions on likely causes of the error and how they might be fixed. This will benefit Galaxy users with clear and actionable error messages and support staff by reducing the amount of reported, non-system errors.
* ''Expected results:''
** Create a tool for analyzing, identifying, and classifying common error messages from the extensive history of error messages from the main public Galaxy server (https://usegalaxy.org).
*** The diversity and size of this data suggests a machine learning approach, but the specific approach taken would be decided by the student and mentor.
** Extend Galaxy’s tool definition syntax to support defining common error classes and suggested resolutions.
** Update Galaxy’s user interface to display potential resolutions and suggested actions based on the types of errors found in an analysis.
* ''Project Home Page URL:'' [https://galaxyproject.org/ galaxyproject.org]
* ''Project paper reference and URL:'' [https://doi.org/10.1093/nar/gky379 The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update], Enis Afgan et al., ''Nucleic Acids Research'', Volume 46, Issue W1, 2 July 2018, Pages W537–W544, https://doi.org/10.1093/nar/gky379
* ''Knowledge prerequisites:'' programming language(s) to be used, plus any other particular computer science skills needed.
* ''Skill level:'' Medium.
* ''Mentors:''

== Use Galaxy to run Reactome analysis and processes on genomic 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]
**''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).

== Create a software package for use in R to query Reactome’s Graph Database in Neo4J ==

*'''Project Idea Name (Project Name/Lab Name)'''
**''Brief explanation:'' The R programming language has an [https://neo4j.com/developer/r/ existing package] for connection to Neo4J databases. This project’s purpose would be to use this package as a base to create a connection for querying Reactome’s Neo4J [https://www.reactome.org/dev/graph-database graph database] and return data structures for manipulating Reactome pathway and reaction data..
**''Expected results:''Allow R end-users to be able to retrieve Reactome pathway and reaction data for analysis by both pre-written functions and custom queries. Examples of categories for such functions may include pathways and reactions which contain certain genes, proteins, Gene Ontology terms or cross-references to other external databases as well as other useful queries for Reactome end-users.
**''Project Home Page URL:'' [https://reactome.org/ reactome.org].
**''Knowledge prerequisites:'' R Programming Language, Neo4J.
**''Skill level:'' Medium.
**''Mentors:'' Joel Weiser (joel.weiser[AT]oicr.on.ca) and Antonio Fabregat (fabregat[AT]ebi.ac.uk). Robin.haw
Categories: Bio

Meetings

GMOD.org recent changes - Fri, 01/24/2020 - 14:49

← Older revision Revision as of 19:49, 24 January 2020 Line 1: Line 1: −'''The next GMOD meeting will be on [[Jan_2014_GMOD_Meeting|January 16th and 17th 2014]], immediately after [http://www.intlpag.org/ PAG XXII].'''      <center> <center> Line 8: Line 7:  </center> </center>    −GMOD puts on several types of meetings, including semi-annual community meetings and specialized hackathons.  GMOD content is also presented at [[Training and Outreach]] events, run both by GMOD and by other organizations.  All these events are listed on the GMOD [[Calendar]].+GMOD has put on several types of meetings, including semi-annual community meetings and specialized hackathons.  GMOD content is also presented at [[Training and Outreach]] events, run both by GMOD and by other organizations.  All these events are listed on the GMOD [[Calendar]].  Full community meeting happen significantly less often now, as funding for them doesn't really exist.  Targeted hackathons or code fests are more common and frequently happen around other meetings.       Line 155: Line 154:  |} |}    −[[Category:Meetings]]+[[Category:GMOD_Community]] −[[Category:GMOD Community]]+  [[Category:Meetings]] [[Category:Meetings]] Scott
Categories: Bio

gmod.org is OK,

GMOD.org status - Tue, 01/21/2020 - 05:35
Categories: Bio

gmod.org is DOWN, 1579594086

GMOD.org status - Tue, 01/21/2020 - 03:35
Categories: Bio

User:Scott

GMOD.org recent changes - Fri, 01/17/2020 - 15:04

← Older revision Revision as of 20:04, 17 January 2020 Line 1: Line 1:  GMOD Coordinator, software development manager at [http://oicr.on.ca/ The Ontario Institute for Cancer Research]. GMOD Coordinator, software development manager at [http://oicr.on.ca/ The Ontario Institute for Cancer Research].    −Scott graduated from The Ohio State University in 1990 with a B. S. in Chemical Engineering and continued on to the University of California in San Diego for graduate school, where he studied improvements to monoclonal antibody production in industrial processes through cell culture and cell cycle modifications.  Upon earning his Ph. D. in Chemical Engineering, he began work in the software industry, working for MSI/Accelrys, Pangea Systems/DoubleTwist, and Athersys, until finally coming to rest at Cold Spring Harbor Laboratory in [[User:Lstein|Lincoln Stein's]] lab, following Lincoln to [http://oicr.on.ca/ OICR] several years ago.  He is the coordinator and a lead developer of the [[Main_Page|GMOD project]], focusing mainly on core schema and tool development, but is also a developer for [http://wormbase.org/ WormBase] and the [http://alliancegenome.org/ Alliance for Genome Resources].  Scott is a happy husband and father of nineteen year old boy-girl twins.+Scott graduated from The Ohio State University in 1990 with a B. S. in Chemical Engineering and continued on to the University of California in San Diego for graduate school, where he studied improvements to monoclonal antibody production in industrial processes through cell culture and cell cycle modifications.  Upon earning his Ph. D. in Chemical Engineering, he began work in the software industry, working for MSI/Accelrys, Pangea Systems/DoubleTwist, and Athersys, until finally coming to rest at Cold Spring Harbor Laboratory in [[User:Lstein|Lincoln Stein's]] lab, following Lincoln to [http://oicr.on.ca/ OICR] several years ago.  He is the coordinator and a lead developer of the [[Main_Page|GMOD project]], focusing mainly on core schema and tool development, but is also a developer for [http://wormbase.org/ WormBase] and the [http://alliancegenome.org/ Alliance for Genome Resources].  Scott is a happy husband and father of twenty year old boy-girl twins who attend San Diego State University.     Scott can be reached at his email address: [http://mailhide.recaptcha.net/d?k=010I5vtKiZqC1kdmtqmWRRhg==&amp;c=6uiWfNokHIbewa_qGkyAF8Tt0sdX6xy0-BIUTsIkwlA=  sco...]@scottcain.net or Twitter @scottjcain. Scott can be reached at his email address: [http://mailhide.recaptcha.net/d?k=010I5vtKiZqC1kdmtqmWRRhg==&amp;c=6uiWfNokHIbewa_qGkyAF8Tt0sdX6xy0-BIUTsIkwlA=  sco...]@scottcain.net or Twitter @scottjcain. Scott
Categories: Bio

gmod.org is DOWN, 1579262886

GMOD.org status - Fri, 01/17/2020 - 07:35
Categories: Bio

JBrowse Tutorial PAG 2020

GMOD.org recent changes - Sun, 01/12/2020 - 15:11

← Older revision Revision as of 20:11, 12 January 2020 (One intermediate revision by the same user not shown)Line 1: Line 1:  This [[Has topic::JBrowse]] tutorial was presented by [[User:Scott|Scott Cain]] at the [http://www.intlpag.org Plant and Animal Genomes] meeting using JBrowse 1.16.6. This [[Has topic::JBrowse]] tutorial was presented by [[User:Scott|Scott Cain]] at the [http://www.intlpag.org Plant and Animal Genomes] meeting using JBrowse 1.16.6.    −This tutorial assumes a [https://www.virtualbox.org VirtualBox] Ubuntu 18.04 (LTS) instance with the tutorial bundle zip file, also available on Amazon S3: [https://s3.amazonaws.com/jbrowse-tutorials/JBrowse+PAG+2020.ova.bz2 JBrowse PAG 2020.ova.bz2] (about 4GB).+This tutorial assumes a [https://www.virtualbox.org VirtualBox] Ubuntu 18.04 (LTS) instance with the tutorial bundle zip file, also available on Amazon S3: [https://s3.amazonaws.com/jbrowse-tutorials/JBrowse+PAG+2020.ova JBrowse PAG 2020.ova] (about 4GB) or [https://jbrowse-tutorials.s3.amazonaws.com/PAG_2020_JBrowse.zip PAG_2020_JBrowse.zip] (about 36MB) for just the JBrowse source and data files for this tutorial.     == Prerequisites == == Prerequisites == Scott
Categories: Bio

User:Kim rutherford

GMOD.org recent changes - Sat, 01/11/2020 - 00:17

← Older revision Revision as of 05:17, 11 January 2020 (2 intermediate revisions by the same user not shown)Line 1: Line 1:     = Current work = = Current work = −I work as a programmer for [https://www.pombase.org/ PomBase] - the pombe genome database, based in Cambridge, UK.  I look after the [https://www.pombase.org PomBase website], the pombe [[Chado]] database and I work on the [[Canto]] community curation tool.+I work as a programmer for [https://www.pombase.org/ PomBase] - the pombe genome database at the [https://www.bioc.cam.ac.uk/ Department of Biochemistry], [https://en.wikipedia.org/wiki/Cambridge Cambridge].  I look after the [https://www.pombase.org PomBase website], the pombe [[Chado]] database and I work on the [[Canto]] community curation tool.     = Previous work = = Previous work = −In the past I worked on [https://www.sanger.ac.uk/resources/software/artemis/ Artemis] at the [http://www.sanger.ac.uk Sanger Institute] and [[InterMine]] at the [http://www.sysbiol.cam.ac.uk Systems Biology Centre], University of Cambridge, UK.+In the past I worked on [https://www.sanger.ac.uk/science/tools/artemis Artemis] at the [http://www.sanger.ac.uk Sanger Institute] and [[InterMine]] at the [http://www.sysbiol.cam.ac.uk Systems Biology Centre], University of Cambridge, UK.    −More recently I worked as a bioinformatics odd job man for the [http://anatomy.otago.ac.nz/ Department of Anatomy], [http://www.otago.ac.nz/ University of Otago], Dunedin, NZ.  I spent part of my time helping with the [https://www.biorxiv.org/content/10.1101/867069v1 tuatara genome project].   +More recently I worked as a bioinformatics odd job man for the [http://anatomy.otago.ac.nz/ Department of Anatomy], [http://www.otago.ac.nz/ University of Otago], [https://en.wikipedia.org/wiki/Dunedin Dunedin], [https://en.wikipedia.org/wiki/New_Zealand New Zealand].  I spent part of my time helping with the [https://www.biorxiv.org/content/10.1101/867069v1 tuatara genome project].        = Contact = = Contact = −I can be contacted at [mailto:kmr44@cam.ac.uk kmr44@cam.ac.uk] or [mailto:kmr@kmr.nz kmr@kmr.nz].+I can be contacted at [mailto:kmr44@cam.ac.uk kmr44@cam.ac.uk] or [mailto:kmr@kmr.nz kmr@kmr.nz].  I work remotely from [https://en.wikipedia.org/wiki/Dunedin Dunedin].     I occasionally [https://twitter.com/kim_rutherford/ post on Twitter] and I have a small web site for my [https://kmr.nz CV]: I occasionally [https://twitter.com/kim_rutherford/ post on Twitter] and I have a small web site for my [https://kmr.nz CV]: Kim rutherford
Categories: Bio

JBrowse Tutorial PAG 2020

GMOD.org recent changes - Fri, 01/10/2020 - 14:49

‎Using Plugins

← Older revision Revision as of 19:49, 10 January 2020 (4 intermediate revisions by the same user not shown)Line 12: Line 12:     It's probably a good idea to use a browser like Chrome or Firefox that has the ability to turn off caching while working on this tutorial.  To do this in Chrome, with the browser open to the JBrowse page you're working on, select Developer->Javascript Console from the View menu.  In the console, click the "gear" icon (settings) and check the box labeled "Disable Cache". It's probably a good idea to use a browser like Chrome or Firefox that has the ability to turn off caching while working on this tutorial.  To do this in Chrome, with the browser open to the JBrowse page you're working on, select Developer->Javascript Console from the View menu.  In the console, click the "gear" icon (settings) and check the box labeled "Disable Cache".  +  +A few basic packages were installed before JBrowse via <code>apt-get</code>:  +  +<span class="enter">  +  sudo apt-get install build-essential zlib1g-dev apache2 curl  +</span>  +  +Also, a few items were installed that aren't needed for this tutorial but would be necessary if you wanted to add plugins (git and NodeJS):  +  +<span class="enter">  +  curl -sL https://deb.nodesource.com/setup_13.x | sudo -E bash -  +  sudo apt-get install -y nodejs  +  sudo apt-get install git  +</span>     == JBrowse Introduction == == JBrowse Introduction == Line 30: Line 44:     <pre class="dont"> <pre class="dont"> −  ##curl -O https://s3.amazonaws.com/jbrowse-tutorials/PAG_2020_JBrowse.zip</span> #that's a capital dash"O" not a zero/zed.+  ##curl -O https://s3.amazonaws.com/jbrowse-tutorials/PAG_2020_JBrowse.zip #that's a capital dash"O" not a zero/zed.  </pre> </pre>  +<pre class="dont">    <span class="enter">cp ~/PAG_2020_JBrowse.zip . ## if we don't need to update the zip file   <span class="enter">cp ~/PAG_2020_JBrowse.zip . ## if we don't need to update the zip file    <span class="enter">unzip PAG_2020_JBrowse.zip</span>   <span class="enter">unzip PAG_2020_JBrowse.zip</span>    <span class="enter">cd PAG_2020_JBrowse   <span class="enter">cd PAG_2020_JBrowse  +</pre>  <pre class="dont"> <pre class="dont">    unzip jbrowse-1.16.6-release.zip   unzip jbrowse-1.16.6-release.zip Line 42: Line 58:  * run <code>setup.sh</code> to configure this copy of JBrowse * run <code>setup.sh</code> to configure this copy of JBrowse    −  <span class="enter">cd ../jbrowse</span>+  <span class="enter">cd jbrowse</span>  <pre class="dont"> <pre class="dont">    ./setup.sh   ./setup.sh Line 382: Line 398:  <syntaxhighlight lang="javascript"> <syntaxhighlight lang="javascript">         {        { −         "type" : "CanvasFeatures",+         "key" : "RepeatMasker",           "trackType" : "CanvasFeatures",          "trackType" : "CanvasFeatures",  +        "storeClass" : "JBrowse/Store/SeqFeature/NCList",           "style" : {          "style" : {               "color" : "function(feature) { var name = feature.get('Name'); if (name.match('Low_complexity') ) { return 'red'; } return 'black';  }",              "color" : "function(feature) { var name = feature.get('Name'); if (name.match('Low_complexity') ) { return 'red'; } return 'black';  }", Line 397: Line 414:             "label" : "Search for {name} at Google",            "label" : "Search for {name} at Google",             "title" : "function(track,feature,div) { return 'Searching for '+feature.get('name')+' at Google'; }"            "title" : "function(track,feature,div) { return 'Searching for '+feature.get('name')+' at Google'; }" −         },+        },  +        "label" : "repeat masker",  +         "urlTemplate" : "tracks/repeat masker/{refseq}/trackData.json",           "compress" : 0,          "compress" : 0, −         "storeClass" : "JBrowse/Store/SeqFeature/NCList",+         "type" : "CanvasFeatures" −        "label" : "repeatmasker",+ −        "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json",+ −        "key" : "RepeatMasker"+         },        },  </syntaxhighlight> </syntaxhighlight> Line 419: Line 435:     RegexSequenceSearch    RegexSequenceSearch    −and the RegexSequenceSearch plugin is already activated (look under the "Track" menu for it).  We will turn on the NeatHTMLFeatures plugin. Right now the Genes track has relatively "boring" glyphs composed of pink rectangles connected by black lines. To turn on NeatHTMLFeatures, just add+and the RegexSequenceSearch plugin is already activated (look under the "Track" menu for it).  We will turn on the HideTrackLabels plugin. Open <code>jbrowse.conf</code>:    −    "plugins": [ +<span class="enter"> −      'NeatHTMLFeatures'+  gedit jbrowse.conf −    ],+</span>    −to the top of <code>data/trackList.json</code>, just inside the first open curly brace.  Reload JBrowse and turn on the Genes track if it isn't already and see the wonder of the psuedo-3D gene glyphs.+and find (cntl-F) "plugins", which will look like this:  +   +<pre>  +## uncomment and edit the example below to enable one or more  +## JBrowse plugins  +# [ plugins.MyPlugin ]  +# location = plugins/MyPlugin  +# [ plugins.AnotherPlugin ]  +# location = ../plugin/dir/someplace/else  +</pre>  +   +Add below this a few lines to active the HideTrackLabels plugin:  +   +<pre>  +[ plugins.HideTrackLabels ]  +location = plugins/HideTrackLabels  +</pre>    −Note that not all plugins are activated this way: typically, if the plugin modifies the way tracks look, it will go here.  If it modifies the way JBrowse *works*, it will go in the <code>jbrowse.conf</code> file.+Note that not all plugins are activated this way: typically, if it modifies the way JBrowse *works*, it will go here.  If the plugin modifies the way tracks look will go in the <code>trackList.json</code> file.     == JBrowse Features == == JBrowse Features == Scott
Categories: Bio

JBrowse Tutorial PAG 2020

GMOD.org recent changes - Fri, 01/10/2020 - 14:49

‎Using Plugins

← Older revision Revision as of 19:49, 10 January 2020 (7 intermediate revisions by the same user not shown)Line 12: Line 12:     It's probably a good idea to use a browser like Chrome or Firefox that has the ability to turn off caching while working on this tutorial.  To do this in Chrome, with the browser open to the JBrowse page you're working on, select Developer->Javascript Console from the View menu.  In the console, click the "gear" icon (settings) and check the box labeled "Disable Cache". It's probably a good idea to use a browser like Chrome or Firefox that has the ability to turn off caching while working on this tutorial.  To do this in Chrome, with the browser open to the JBrowse page you're working on, select Developer->Javascript Console from the View menu.  In the console, click the "gear" icon (settings) and check the box labeled "Disable Cache".  +  +A few basic packages were installed before JBrowse via <code>apt-get</code>:  +  +<span class="enter">  +  sudo apt-get install build-essential zlib1g-dev apache2 curl  +</span>  +  +Also, a few items were installed that aren't needed for this tutorial but would be necessary if you wanted to add plugins (git and NodeJS):  +  +<span class="enter">  +  curl -sL https://deb.nodesource.com/setup_13.x | sudo -E bash -  +  sudo apt-get install -y nodejs  +  sudo apt-get install git  +</span>     == JBrowse Introduction == == JBrowse Introduction == Line 30: Line 44:     <pre class="dont"> <pre class="dont"> −  ##curl -O https://s3.amazonaws.com/jbrowse-tutorials/PAG_2020_JBrowse.zip</span> #that's a capital dash"O" not a zero/zed.+  ##curl -O https://s3.amazonaws.com/jbrowse-tutorials/PAG_2020_JBrowse.zip #that's a capital dash"O" not a zero/zed.  </pre> </pre>  +<pre class="dont">    <span class="enter">cp ~/PAG_2020_JBrowse.zip . ## if we don't need to update the zip file   <span class="enter">cp ~/PAG_2020_JBrowse.zip . ## if we don't need to update the zip file    <span class="enter">unzip PAG_2020_JBrowse.zip</span>   <span class="enter">unzip PAG_2020_JBrowse.zip</span>    <span class="enter">cd PAG_2020_JBrowse   <span class="enter">cd PAG_2020_JBrowse  +</pre>  <pre class="dont"> <pre class="dont"> −  unzip jbrowse-1.16.1-release.zip+  unzip jbrowse-1.16.6-release.zip −  mv jbrowse-1.16.1-release jbrowse+  mv jbrowse-1.16.6-release ../jbrowse  </pre> </pre>    Line 382: Line 398:  <syntaxhighlight lang="javascript"> <syntaxhighlight lang="javascript">         {        { −         "type" : "CanvasFeatures",+         "key" : "RepeatMasker",           "trackType" : "CanvasFeatures",          "trackType" : "CanvasFeatures",  +        "storeClass" : "JBrowse/Store/SeqFeature/NCList",           "style" : {          "style" : {               "color" : "function(feature) { var name = feature.get('Name'); if (name.match('Low_complexity') ) { return 'red'; } return 'black';  }",              "color" : "function(feature) { var name = feature.get('Name'); if (name.match('Low_complexity') ) { return 'red'; } return 'black';  }", Line 397: Line 414:             "label" : "Search for {name} at Google",            "label" : "Search for {name} at Google",             "title" : "function(track,feature,div) { return 'Searching for '+feature.get('name')+' at Google'; }"            "title" : "function(track,feature,div) { return 'Searching for '+feature.get('name')+' at Google'; }" −         },+        },  +        "label" : "repeat masker",  +         "urlTemplate" : "tracks/repeat masker/{refseq}/trackData.json",           "compress" : 0,          "compress" : 0, −         "storeClass" : "JBrowse/Store/SeqFeature/NCList",+         "type" : "CanvasFeatures" −        "label" : "repeatmasker",+ −        "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json",+ −        "key" : "RepeatMasker"+         },        },  </syntaxhighlight> </syntaxhighlight> Line 419: Line 435:     RegexSequenceSearch    RegexSequenceSearch    −and the RegexSequenceSearch plugin is already activated (look under the "Track" menu for it).  We will turn on the NeatHTMLFeatures plugin. Right now the Genes track has relatively "boring" glyphs composed of pink rectangles connected by black lines. To turn on NeatHTMLFeatures, just add+and the RegexSequenceSearch plugin is already activated (look under the "Track" menu for it).  We will turn on the HideTrackLabels plugin. Open <code>jbrowse.conf</code>:    −    "plugins": [ +<span class="enter"> −      'NeatHTMLFeatures'+  gedit jbrowse.conf −    ],+</span>    −to the top of <code>data/trackList.json</code>, just inside the first open curly brace.  Reload JBrowse and turn on the Genes track if it isn't already and see the wonder of the psuedo-3D gene glyphs.+and find (cntl-F) "plugins", which will look like this:  +   +<pre>  +## uncomment and edit the example below to enable one or more  +## JBrowse plugins  +# [ plugins.MyPlugin ]  +# location = plugins/MyPlugin  +# [ plugins.AnotherPlugin ]  +# location = ../plugin/dir/someplace/else  +</pre>  +   +Add below this a few lines to active the HideTrackLabels plugin:  +   +<pre>  +[ plugins.HideTrackLabels ]  +location = plugins/HideTrackLabels  +</pre>    −Note that not all plugins are activated this way: typically, if the plugin modifies the way tracks look, it will go here.  If it modifies the way JBrowse *works*, it will go in the <code>jbrowse.conf</code> file.+Note that not all plugins are activated this way: typically, if it modifies the way JBrowse *works*, it will go here.  If the plugin modifies the way tracks look will go in the <code>trackList.json</code> file.     == JBrowse Features == == JBrowse Features == Scott
Categories: Bio

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