Difference between revisions of "GSoC"

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=='''Welcome to the Genome Informatics GSoC'''==
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[[File:GoogleSummer_2016logo.jpg|373px|right|link=GSoC]]
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''“Google Summer of Code (GSoC) is a global program that offers student developers stipends to write code for various open source software projects. We have worked with several open source, free software, and technology-related groups to identify and fund several projects over a three month period. Since its inception in 2005, the program has brought together over 4,500 students and more than more than 4,000 mentors & co-mentors from over 85 countries worldwide, all for the love 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.”''<br>
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GSoC has several goals:
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== Google Summer of Code 2019 @ Open Genome Informatics ==
  
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*get more open source code created and released for the benefit of all
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'''[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]'')
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*inspire young developers to begin participating in open source development
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*help open source projects identify and bring in new developers and committers
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*provide students the opportunity to do work related to their academic pursuits during the summer
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*give students more exposure to real-world software development scenarios.
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[http://socghop.appspot.com Google Summer of Code (GSoC)]
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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].
  
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===='''About Genome Informatics GSoC'''====
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'''More information about this year's participating bioinformatics groups can be found [[GSOC_Groups | here]].'''
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The Genome Infomatics group is organizing the joint efforts of WormBase, Reactome, and GBrowse (see below). This is a great opportunity for students to contribute to the work of three different bioinformatics projects.<br>
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'''[http://www.wormbase.org Wormbase]''' is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. The database is constantly updated and new versions are released on a monthly basis. WormBase is a collaboration among the Wellcome Trust Sanger Institute, Ontario Institute for Cancer Research, Washington University in St. Louis, and the California Institute of Technology. Links: [http://www.wormbase.org Website].<br>
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To learn more about this year's event and how GSoC works, please refer to the [https://developers.google.com/open-source/gsoc/faq FAQ].
  
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'''[http://www.reactome.org Reactome]''' is a manually curated database of core pathways and reactions in human biology that functions as a data mining resource and electronic textbook. The Reactome data model describes diverse processes in the human system, including the pathways of intermediary metabolism, regulatory pathways, signal transduction, and high-level processes, such as the cell cycle. Reactome software uses only freely available (and often open source) components and has been created with cross-platform compatibility and wide usability in mind. Data is stored in a MySQL database, the web site is implemented in Perl and data entry tool in Java programming language. The Reactome team is composed of individuals who are both biologists and programmers at the Ontario Institute for Cancer Research, New York University Langone Medical Center, Cold Spring Harbor Laboratory, and The European Bioinformatics Institute. Links: [http://www.reactome.org Website], [http://wiki.reactome.org ReactomeWiki ].<br>
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==Mailing lists, IRC, and other ways to get in touch  ==
  
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'''[http://www.gmod.org Generic Model Organism Database (GMOD)]''' is an open source project to develop a complete set of software for creating and administering a model organism database. Components of this project include genome visualization and editing tools, literature curation tools, a robust database schema, biological ontology tools, and a set of standard operating procedures. This project is collaboration of several database projects, including WormBase, FlyBase, Mouse Genome Informatics, Gramene, the Rat Genome Database, TAIR, EcoCyc, and the Saccharomyces Genome Database. Links: [http://www.gmod.org Website], [http://blog.gmod.org GMOD Blog]<br>
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*Email: [mailto:robin.haw@oicr.on.ca robin.haw@oicr.on.ca] '''and''' [mailto:help@gmod.org help@gmod.org] -- find out more about GSoC, a specific project, or your potential mentor(s).
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===='''Contact Us'''====
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*Email: robin.haw[AT]oicr.on.ca - contact me to find out more about a project or your potential mentor(s).
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*Discussion mailing lists: [http://groups.google.com/group/genome-informatics Genome Informatics Google Groups] - ask about our projects; join the community!
 
*Discussion mailing lists: [http://groups.google.com/group/genome-informatics Genome Informatics Google Groups] - ask about our projects; join the community!
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*IRC channel: #genomeinformatics on Freenode.
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* Students and Mentors can email both [[User:Robin.haw|Robin]] and [[User:Scott|Scott]] to get more information about the program.
  
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===='''How to apply'''====
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== [[GSOC_Project_Ideas_2019 | Project Ideas]] ==
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We would like to know who you are and how you think. Incorporate the following into your application:
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*Your information
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**Name, email, and website (optional)
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*Brief background: education and relevant work experience
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*Your programming interests and strengths
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**What are your languages of choice?
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**Any prior experience with open source development?
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**Your interest and background in biology or bioinformatics
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**Any prior exposure to biology or bioinformatics?
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*Your ideas for a project (an original idea or one expanded from our Ideas Page)
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**Provide as much detail as possible
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**Strong applicants include an implementation plan and timeline (hint!)
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**Refer to and link to other projects or products that illustrate your ideas
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**Identify possible hurdles and questions that will require more research/planning
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*What can you bring to the team?
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===='''Guidelines and Advice'''====
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*[http://www.booki.cc/gsocstudentguide GSoC Student Guide]
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*[http://www.google-melange.com/document/show/gsoc_program/google/gsoc2011/faqs#applying Application Guidelines]
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*[http://code.google.com/p/google-summer-of-code/wiki/AdviceforStudents Advice for Student Applicants]
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===='''Project Ideas'''====
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As we are developing new features for WormBase, Reactome and GBrowse, we are exploring a number of areas ideal for Google Summer of Code students. These projects include a broad set of skills, technologies and domains, such as GUIs, database integration and algorithms. You are also encouraged to propose your own ideas related to our projects. If you have strong computer skills and have an interest in biology or bioinformatics, then you should apply!
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====='''IDEA 1: Original Idea'''=====
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Feel free to propose your own idea. As long as it relates to one of our projects, we will give it serious consideration. Creativity and self-motivation are great traits for open source programmers, but make sure your proposal is also relevant.
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====='''IDEA 2: Export Reactome layout in BioPAX'''=====
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It is difficult to exchange pathway layout or diagrams among different pathway databases. BioPAX is a pathway exchange format, but without support of pathway diagram. In this project, we propose to create an XML file format for visualization based on Reactome pathway diagrams for BioPAX level 2 and 3 exports, and a Java applet or Web Start visualization tool based on our curator tool to display this format.
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Language and Skills:  Java, XML, OWL and BioPAX<br>
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Idea by: Guanming Wu<br>
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Potential Mentors: Guanming Wu<br>
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====='''IDEA 3: HTML 5 canvas based visualization tool for pathways and networks'''=====
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With modern browsers' support of HTML5 canvas, it is a time to develop a canvas-based, dynamic visualization tool for biological interaction networks and pathways based on the new canvas tag. In this project, we propose to develop a canvas-based network interaction visualization prototype that can run in both modern browsers in a full-fledged computer, or in a tablet (e.g. ipad). The whole ideas are based on these two canvas based web applications: [http://www.canvasdemos.com/2010/08/05/lucidchart/ LucidChart] and [http://dev.opera.com/articles/view/html5-canvas-painting/ HTML 5 canvas painting].
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Language and Skills: HTML5 (esp canvas), JavaScript, Java, GWT<br>
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Idea by: Guanming Wu<br>
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Potential Mentors: Guanming Wu, Robin Haw and Marc Gillespie<br>
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====='''IDEA 4: Cytoscape Web based visualization tool'''=====
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This would reuse server-side code to replace the Reactome pathway browser.
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Language and Skills: GWT<br>
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Idea by: David Croft<br>
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Potential Mentors: David Croft and Guanming Wu<br>
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====='''IDEA 5: Pathway Summary visualization'''=====
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Provides a user with an overview of all of the pathways in Reactome, able to show expression and species comparison information in a multi-pathway context.
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Language and Skills: GWT<br>
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Idea by: David Croft<br>
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Potential Mentors: David Croft<br>
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====='''IDEA 6: Reactome RESTful API'''=====
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It is crucial to have a nice API for Reactome so that  the Reactome annotated data can be used programmatically and integrated in other web applications (e.g. Wormbase) easily with very low maintenance. In this project, we propose to develop a Reactome RESTful API which should be lightweight, easy to use, and well-documented.
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Language and Skills:RESTful Web Service, Java, Jersey , MySQL<br>
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'''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.
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Idea by: Guanming Wu<br>
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Potential Mentors: Guanming Wu<br>
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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.
  
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====='''IDEA 7: Chado RESTful API'''=====
 
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[[Chado]] is the database schema underlying several GMOD projects, and there are many installed instances around the world.  Having a RESTful API would allow both the creation of "mashup" sites that pull data from various Chado instances but would also facilitate data sharing between sites that have Chado installed.
 
  
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Language and Skills: RESTful Web Service, Perl (Dancer or Catalyst), PostgreSQL<br>
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== Preparing for GSoC 2019 ==
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Idea by: [[User:Scott|Scott Cain]]<br>
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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.
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Potential Mentors: [[User:Scott|Scott Cain]], [[User:Jogoodma|Josh Goodman]]
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===='''Resources'''====
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===Students===
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*[http://socghop.appspot.com GSoC Main Site]
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More information about [[GSOC_Applications_Guide | writing your application]] will be available closer to the start of the student application period.
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*[http://code.google.com/p/google-summer-of-code/wiki/GsocFlyers#2011_Flyers This year's flyer]
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*[http://code.google.com/p/google-summer-of-code/wiki/ProgramPresentations GSoC Presentations]
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*[http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2011/faqs Program FAQ]
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*[http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2011/faqs#timeline Program Timeline]
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*[http://groups.google.com/group/google-summer-of-code-discuss GSoC Discussion List]
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*[http://groups.google.com/group/google-summer-of-code-announce Announcement List]
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*[http://www.youtube.com/user/googOSPOstudntprgrms GSoC YouTube Channel]
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*[http://google-opensource.blogspot.com/ GSoC Blog]
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====='''For Students'''=====
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===Mentors===
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*[http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2010/faqs#payments When do I get paid?!]
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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.
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*[http://code.google.com/p/google-summer-of-code/wiki/AdviceforStudents Advice for Student Applicants]
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*[http://groups.google.com/group/google-summer-of-code-students-list GSoC Students-Only List]
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====='''For Mentors'''=====
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[[Category:Galaxy]]
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*[http://socghop.appspot.com/ GSoC Main Site]
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[[Category:JBrowse]]
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*[http://en.flossmanuals.net/GSoCMentoringGuide Mentoring: The Book]
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[[Category:MGI]]
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*[http://code.google.com/p/google-summer-of-code/wiki/AdviceforMentors Advice for Mentors]
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[[Category:WormBase]]
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*[http://groups.google.com/group/google-summer-of-code-mentors-list GSoC Mentors-Only List]
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[[Category:GSoC]]
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[[Category:Reactome]]
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[[Category:WebApollo]]

Revision as of 17:09, 18 December 2018

GoogleSummer 2016logo.jpg

Google Summer of Code 2019 @ Open Genome Informatics

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 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 GMOD and its software projects -- JBrowse, Apollo, Chado, Galaxy etc.; Mouse Genome Informatics; OICR; Reactome; WormBase; and Bioconda.

More information about this year's participating bioinformatics groups can be found here.

To learn more about this year's event and how GSoC works, please refer to the FAQ.

Mailing lists, IRC, and other ways to get in touch

Project Ideas

Got an idea for a GSOC project? 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.


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 2019 mentoring organization until 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

More information about writing your application will be available closer to the start of the student application period.

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 advice about mentoring and other resources are available.

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