http://gmod.org/mediawiki/api.php?action=feedcontributions&user=Ericiam&feedformat=atomGMOD - User contributions [en]2024-03-29T12:07:44ZUser contributionsMediaWiki 1.23.13http://gmod.org/wiki/2018_PAG_Hackathon2018 PAG Hackathon2018-01-12T01:06:13Z<p>Ericiam: add node</p>
<hr />
<div>The GMOD hackathon will take place January 10-11, 2018 (a few days before PAG, but not on January 12 so as not to overlap with the [[Tripal]] user meeting). It will take place at the [https://az760333.vo.msecnd.net/-/media/property/town-and-country/tcpropertymap-with-points.pdf Town and Country Hotel] in the Brittany room. The Brittany room is in the eastern edge of the property in the north/south center, off of the Regency Courtyard). We expect that topics will include [[JBrowse]] (server-side stuff and plugins), Galaxy connectivity and plugins, and Tripal plugins (this hackathon overlaps the [[Tripal]] hackathon and user meeting that runs January 11-12).<br />
<br />
Registration is $50 which covers part of the fee for the room (where the rest is made up from the kind JBrowse folks) and lunch on the first day. Please use the [https://www.eventbrite.com/e/gmod-2018-pag-hackathon-tickets-39700164260 Eventbrite page] to register and pay.<br />
<br />
==Suggested Topics==<br />
<br />
# <strike>Improving the [https://github.com/galaxy-genome-annotation/python-apollo Python library] for interacting with the [http://demo.genomearchitect.org/Apollo2/WebServices/ Apollo API]</strike><br />
##Done! PRs: [https://github.com/galaxy-genome-annotation/python-apollo/pull/6 1], [https://github.com/galaxy-genome-annotation/python-apollo/pull/8 2]<br />
# Adding an “Instructor” role to facilitate the usage of Apollo in an educational setting [https://github.com/GMOD/Apollo/issues/1178] (working on)<br />
##A list of what permissions the instructor role would have would be very useful. Siloed by organism?<br />
# Incorporating additional metadata to an organism in [https://github.com/GMOD/Apollo/issues/1834 Apollo to facilitate integration with Galaxy Histories] (resolved)<br />
# [http://www.internationalgenome.org/faq/what-are-cram-files/ CRAM] support for [https://github.com/GMOD/jbrowse/issues/546 JBrowse] and [https://github.com/GMOD/jbrowse/issues/926 CRAI indexes] and [https://github.com/GMOD/Apollo/issues/550 extend to Apollo].<br />
##Might not be hard, but we don't know<br />
# Customize BAM tracks in Apollo: [https://github.com/GMOD/Apollo/issues/1031 original from last hackathon] (resolved)<br />
# <strike>Updating table descriptions to generalize mage to include next-gen sequencing experiments and other possible analyses instead of microarray only</strike><br />
##Make issue in Chado add a link for 1.4 outline. See related [https://github.com/GMOD/Chado/issues/25 bug report]<br />
##Done! [https://github.com/GMOD/Chado/pull/50 Pull request]<br />
# <strike>Adding a cvalue_id field to the biomaterialprop table, as is done for the natural diversity module.</strike> This allows the property values to also utilize a cvterm.<br />
##Make an issue in Chado. See the related [https://github.com/GMOD/Chado/issues/26 bug report]<br />
##Done! [https://github.com/GMOD/Chado/pull/54 Pull request]<br />
# Adding track-level permissions to JBrowse tracks in [https://github.com/GMOD/Apollo/issues/17 Apollo] and [https://github.com/GMOD/jbrowse/issues/948 JBrowse] directly. (need to flesh out some policies. Generally, this feature is available with JBServer.)<br />
# Plugin in [https://github.com/GMOD/jbrowse/issues/949 JBrowse] that goes to the next isoform (similar to the behavior in Apollo's manual annotation area).<br />
# Customize BAM tracks. Per Chris Elsik: better filtering (spliced reads on top, sort by score or other attributes, filter unspiced reads)<br />
# Simplify JBrowse minification<br />
# <strike>Get an EST glyph similar to what GBrowse has.</strike> Done! Commits: [https://github.com/WormBase/website-genome-browsers/blob/jbrowse-staging/jbrowse/jbrowse/src/JBrowse/View/FeatureGlyph/LinkedEST.js LinkedEST.js] [https://github.com/WormBase/website-genome-browsers/commit/003e7bf1baf331667c8bb45ecb1826f4b908e1cb Supporting files]<br />
# <strike>Add type_id to analysis table</strike> Done! [https://github.com/GMOD/Chado/pull/52 Pull request]<br />
# <strike>Add linker tables to make working with biomaterials easier</strike> Done! [https://github.com/GMOD/Chado/pull/55 Pull request]<br />
# <strike>Get more organized for 1.4 Chado release</strike> Done! [https://github.com/GMOD/Chado/issues?utf8=%E2%9C%93&q=+label%3A%22Chado+1.4+Suggestion%22+ List of issues to address for 1.4]<br />
<br />
== Resources ==<br />
<br />
* [http://genomearchitect.readthedocs.io/en/latest/Apollo2Build.html Apollo dev guide]<br />
* [https://docs.google.com/document/d/1t_Jb4XxUPtgGRSKtznsqvjTjmR4vpFHPQROMQ0OZK9A/edit?usp=sharing Chado 1.4 suggested additions].<br />
<br />
==Pre-hackathon call notes==<br />
#Can we have a method for people to remotely participate?</div>Ericiamhttp://gmod.org/wiki/2018_PAG_Hackathon2018 PAG Hackathon2017-12-20T23:08:31Z<p>Ericiam: Add references to JBrowse tickets</p>
<hr />
<div>The GMOD hackathon will take place January 10-11, 2018 (a few days before PAG, but not on January 12 so as not to overlap with the [[Tripal]] user meeting). It will take place at the [https://az760333.vo.msecnd.net/-/media/property/town-and-country/tcpropertymap-with-points.pdf Town and Country Hotel] in the Brittany room. The Brittany room is in the eastern edge of the property in the north/south center, off of the Regency Courtyard). We expect that topics will include [[JBrowse]] (server-side stuff and plugins), Galaxy connectivity and plugins, and Tripal plugins (this hackathon overlaps the [[Tripal]] hackathon and user meeting that runs January 11-12).<br />
<br />
Registration is $50 which covers part of the fee for the room (where the rest is made up from the kind JBrowse folks) and lunch on the first day. Please use the [https://www.eventbrite.com/e/gmod-2018-pag-hackathon-tickets-39700164260 Eventbrite page] to register and pay.<br />
<br />
==Suggested Topics==<br />
<br />
# Improving the [https://github.com/galaxy-genome-annotation/python-apollo Python library] for interacting with the [http://demo.genomearchitect.org/Apollo2/WebServices/ Apollo API]<br />
# Adding an “Instructor” role to facilitate the usage of Apollo in an educational setting [https://github.com/GMOD/Apollo/issues/1178]<br />
##A list of what permissions the instructor role would have would be very useful. Siloed by organism?<br />
# Incorporating additional metadata to an organism in [https://github.com/GMOD/Apollo/issues/1834 Apollo to facilitate integration with Galaxy Histories]<br />
# [http://www.internationalgenome.org/faq/what-are-cram-files/ CRAM] support for [https://github.com/GMOD/jbrowse/issues/546 JBrowse] and [https://github.com/GMOD/jbrowse/issues/926 CRAI indexes] and [https://github.com/GMOD/Apollo/issues/550 extend to Apollo].<br />
##Might not be hard, but we don't know<br />
# Customize BAM tracks in Apollo: [https://github.com/GMOD/Apollo/issues/1031 original from last hackathon]<br />
# Updating table descriptions to generalize mage to include next-gen sequencing experiments and other possible analyses instead of microarray only<br />
##Make issue in Chado add a link for 1.4 outline. See related [https://github.com/GMOD/Chado/issues/25 bug report]<br />
# Adding a cvalue_id field to the biomaterialprop table, as is done for the natural diversity module. This allows the property values to also utilize a cvterm.<br />
##Make an issue in Chado. See the related [https://github.com/GMOD/Chado/issues/26 bug report]<br />
# Adding track-level permissions to JBrowse tracks in [https://github.com/GMOD/Apollo/issues/17 Apollo] and [https://github.com/GMOD/jbrowse/issues/948 JBrowse] directly.<br />
# Plugin in [https://github.com/GMOD/jbrowse/issues/949 JBrowse] that goes to the next isoform (similar to the behavior in Apollo's manual annotation area).<br />
# Customize BAM tracks. Per Chris Elsik: better filtering (spliced reads on top, sort by score or other attributes, filter unspiced reads)<br />
<br />
== Resources ==<br />
<br />
* [http://genomearchitect.readthedocs.io/en/latest/Apollo2Build.html Apollo dev guide]<br />
* [https://docs.google.com/document/d/1t_Jb4XxUPtgGRSKtznsqvjTjmR4vpFHPQROMQ0OZK9A/edit?usp=sharing Chado 1.4 suggested additions].<br />
<br />
==Pre-hackathon call notes==<br />
#Can we have a method for people to remotely participate?</div>Ericiamhttp://gmod.org/wiki/Jun_2016_GMOD_MeetingJun 2016 GMOD Meeting2016-07-05T23:09:50Z<p>Ericiam: /* Draft Agenda */</p>
<hr />
<div><center><br />
{| style="vertical-align: middle; border: 2px solid #A6A6BC;" cellpadding="10"<br />
| rowspan="1" | [[Image:GMOD2016ColorsBigLetters_300px.png|300px|center]]<br />
| style="font-size: 170%; line-height: 120%" |<b>2016 GMOD Meeting</b><br /><br />June 30 - July 1, 2016<br />[http://iu.edu/ Indiana University]<br />Bloomington, Indiana, United States <br /><br />[https://gmod2016.eventbrite.com/ Register now] <div style="font-size: 80%; line-height: 80%"><br /><br />[https://twitter.com/search?q=%23GMOD2016 #GMOD2016] &nbsp;&nbsp; [https://twitter.com/gmodproject @gmodproject]</div><br />
|}<br />
</center><br />
<br />
<br />
GMOD will be holding a community meeting on June 30th and July 1st in Bloomington, IN, immediately after the [https://gcc2016.iu.edu/ 2016 Galaxy Community Conference (GCC2016)]. [[Meetings|GMOD Meetings]] are a mix of [[GMOD Membership#Users|user]] and [[GMOD Membership#Developers|developer]] presentations, and are a great place to find out what is happening in the project, what's coming up, and what others are doing.<br />
<br />
<br />
'''[https://gmod2016.eventbrite.com Please register online at Eventbrite by June 20th 2016].''' Early bird registration ends May 21.<br />
<br />
For those who would like to present a talk or poster, the meeting registration form includes a section for submitting the presentation title and abstract.<br />
<br />
If you have any suggestions or requests for the meeting, please contact the [mailto:help@gmod.org GMOD help desk].<br />
<br />
== About GMOD ==<br />
<br />
'''GMOD''' is the Generic Model Organism Database project, a collection of interoperable open-source [[GMOD Components|software components]] for annotating, visualizing, managing and analyzing biological data. GMOD is also an active community of software developers and biologists addressing common challenges with their data.<br />
<br />
The GMOD suite includes widely used tools such as [[GBrowse]] and [[JBrowse]] (and [[WebGBrowse]]) for genome browsing, [[Apollo]], [[Canto]] and [[MAKER]] for genome annotation, [[GBrowse_syn]] and [[CMap]] for comparative genomics visualization, [[Chado]], [[BioMart]] and [[InterMine]] for data integration, management, and querying, and [[Galaxy]] and [[Ergatis]] (and [[ISGA]]) for data analysis.<br />
<br />
<!-- ==Keynote Speaker==<br />
<br />
<div class="emphasisbox"><br />
To be announced<br />
</div><br />
--><br />
<br />
==Registration==<br />
<br />
Please [https://gmod2016.eventbrite.com/ register online at EventBrite]. Early bird registration ends May 30th.<br />
<br />
The registration fee includes lunch on June 30th.<br />
<br />
==Draft Agenda==<br />
<br />
===Walnut room, Thursday, June 30===<br />
<br />
<br />
{| class="wikitable"<br />
! Time<br />
! Topic<br />
! Presenter(s)<br />
! Presentation<br />
|-<br />
|08:50 <br />
|Pre-meeting continental breakfast<br />
|<br />
|<br />
|-<br />
|09:15<br />
| Introductions<br />
| <br />
|<br />
|-<br />
|09:40 <br />
| The State of GMOD<br />
|[[User:Scott|Scott Cain]]<br />
| [[Media:GMOD2016_GMOD.pdf|Intro]], [[Media:GMOD2016_InterMine.pdf|InterMine]], [https://www.dropbox.com/s/7i39svwlegfr4rq/MAKER_GMOD_2016.pdf?dl=0 MAKER]<br />
|-<br />
|10:10<br />
| Introduction to uMOD<br />
|[[User:Scott|Scott Cain]]<br />
| [[Media:GMOD2016_uMOD.pdf|Slides]]<br />
|-<br />
|10:35<br />
| Coffee<br />
|<br />
|<br />
|-<br />
|10:50<br />
| GMOD in Action: The Legume Federation Project <br />
| Ethalinda Cannon<br />
| [[Media:LegFed_GMOD2016.pdf|Slides]]<br />
|-<br />
|11:20 <br />
| [[JBrowse]] Update<br />
| Eric Yao<br />
| [https://drive.google.com/a/berkeley.edu/file/d/0BzJAAJpIcu9hVFloS2R6ZUxhcUE/view?usp=sharing Slides]<br />
|-<br />
|11:50 <br />
|Lunch<br />
|<br />
|<br />
|-<br />
|1:00 <br />
| [[Apollo]]: Collaborative Manual Annotation in the GMOD Workflow<br />
| Nathan Dunn<br />
|<br />
|-<br />
|1:30 <br />
| [[Tripal]] Update<br />
| Lacey-Anne Sanderson<br />
|<br />
|-<br />
|2:30 <br />
|Coffee<br />
|<br />
|<br />
|-<br />
|2:45 <br />
|[[Galaxy]] Update <br />
|[[User:Clements|Dave Clements]], [https://github.com/bgruening Bjöern Grüning]<br />
| [[:File:GMOD2016_Galaxy.pdf|Slides]]<br />
|-<br />
|3:15 <br />
|EvidentialGene project at http://eugenes.org/EvidentialGene/<br />
| Don Gilbert<br />
| [http://arthropods.eugenes.org/EvidentialGene/about/evigenegmod1606iu.pdf Slides]<br />
|-<br />
|3:45 <br />
| FlyBase Update and Chado discussion<br />
|[[User:Jogoodma|Josh Goodman]]<br />
|<br />
|}<br />
<br />
===Friday, July 1===<br />
<br />
{| class="wikitable"<br />
! Time<br />
! Topic<br />
! Presenter(s)<br />
! Presentation<br />
|-<br />
|08:50 <br />
|Pre-meeting continental breakfast<br />
|<br />
|<br />
|-<br />
|09:15<br />
|Tripal Expression module and search<br />
|Meg Staton<br />
|[[:File:GMOD_Staton.pdf|Slides]]<br />
|-<br />
|09:45<br />
| Lightning talks, including Asela Dassanayake, Eric Rasche and Thoba Lose<br />
|<br />
|[[Media:GMOD_Asela.pdf|Asela/LanzaTech]]<br />
|-<br />
|11:30 <br />
|Lunch (on your own)<br />
|<br />
|<br />
|-<br />
|1:00<br />
| Tripal workshop<br />
|<br />
|<br />
|}<br />
<br />
==Agenda items==<br />
<br />
More to be added as we confirm more speakers. If you are interested in giving a talk please contact the [mailto:help@gmod.org GMOD help desk].<br />
<br />
* GMOD project updates, including [[Tripal]], [[Galaxy]], [[JBrowse]], [[Chado]], [[MAKER]].<br />
* Introduction to umod ([[User:Scott|Scott Cain]])<br />
* "Apollo: Collaborative Manual Annotation in the GMOD Workflow" (Nathan Dunn)<br />
* Tripal update (Lacey Sanderson)<br />
* Tripal Expression module and search (Ming Chen)<br />
* EvidentialGene project at http://eugenes.org/EvidentialGene/ ([[User:Dongilbert|Don Gilbert]])<br />
* DictyBase on using and extending GMOD tools (Chado, JBrowse) and new infrastructure(docker and possibly kubernetes) (Siddhartha Basu)<br />
* GMOD in Action: The Legume Federation Project (Ethalinda Cannon)<br />
*[[Tripal]] Workshop (Friday afternoon)<br />
<br />
==Logistics==<br />
<br />
If you require lodging, we have partnered with the [https://gcc2016.iu.edu/ 2016 Galaxy Community Conference], please go here: [https://indianauniv.ungerboeck.com/prod/SignIn.aspx?ReturnUrl=%2fprod%2femc00%2fregister.aspx%3fOrgCode%3d10%26EvtID%3d6925%26AppCode%3dREG&OrgCode=10&EvtID=6925&DictSeq=27&Lang=*&AppCode=REG&CultureInfo=en-US GCC16 registration page] .<br />
<br />
You DO NOT have to register for the GCC2016 conference to utilize housing. Just check HOUSING ONLY when registering.<br />
<br />
=== Shared Rides ===<br />
<br />
Please put your travel times [https://docs.google.com/spreadsheets/d/1sBD74e9DTldNshPgZzRNQspts1f9pASjMww105-m-5s/edit#gid=0 here].<br />
<br />
<br />
<center><br />
<div class="emphasisbox"><br />
<div style="font-size: 115%">"It's tempting to see bioinformatics as a collection of potential problems. Being at a GMOD meeting helps us see bioinformatics as a collection of potential solutions."</div><br />
<div style="padding-top: 0.5em">Isabelle Phan, [http://www.seattlebiomed.org SBRI], and past GMOD meeting participant</div><br />
</div><br />
</center><br />
<br />
<center>(Thanks to [[User:Clements|Dave Clements]] for the nice logo)</center><br />
<br />
[[Category:Meetings]]<br />
[[Category:GMOD Community]]</div>Ericiamhttp://gmod.org/wiki/GSOC_Project_Ideas_2016GSOC Project Ideas 20162016-02-18T00:19:04Z<p>Ericiam: tweak idea 2</p>
<hr />
<div>There are plenty of challenging and interesting project ideas this year. These projects include a broad set of skills, technologies and domains, such as GUIs, database integration and algorithms. <br />
<br />
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. <br />
<br />
*'''Project Idea Name'''<br />
**''Brief explanation:'' Brief description of the idea, including any relevant links, etc. <br />
**''Expected results:'' describe the outcome of the project idea.<br />
**''Knowledge prerequisites:'' programming language(s) to be used, plus any other particular computer science skills needed.<br />
**''Skill level:'' Basic, Medium or Advanced.<br />
**''Mentors:'' name + contact details of the lead mentor, name + contact details of backup mentor.<br />
<br />
<br />
Here is a list of the proposed project ideas for 2016:<br />
<br />
*'''Project Idea 1: Biological Graph Visualization'''<br />
**''Brief explanation:'' Tripal (http://tripal.info) is an open-source suite of Drupal modules that allows a scientific research community to more easily setup and manage a data repository for genomic, genetic and related biological data. It provides data pages, data mining tools and visualizations. Tripal is used or in development by over 25 different genome database websites, and is developed by an international group. A Tripal module currently exists for importing, searching and visualizing graph data that models the "network" of interactions of various components of a biological system. However, the module is not complete and requires improvements to the visualizations. The goal of this project would be to complete the remaining work for this module such that it can be shared with others.<br />
**''Expected results:'' Once completed, a Drupal module will freely available for Tripal-based sites to use on their own sites. Thus providing graph visualizations for complex biological systems.<br />
**''Knowledge prerequisites:'' PHP, Drupal, JavaScript, SQL.<br />
**''Skill level:'' Medium<br />
**''Mentors:'' Stephen Ficklin<br />
<br />
*'''Project Idea 2: Github-based revision control of synthetic chromosomes'''<br />
**''Brief explanation:'' JBrowse (http://jbrowse.org) is a robust open-source genome visualization tool built around Javascript and HTML5. It has gained wide acceptance among biologists and bioinformatisist with thousands of active installations worldwide in genomic research. This project deals with a module that enables management synthetic DNA sequences in JBrowse. Synthetic biologists design DNA sequences that differ from their analogous sequences in natural organisms. As with code, the differences can be incremental or radical, and can be visualized using “diff”-like tools. And, also as with code, good revision control is fundamentally important. We propose to build module that enables biologists to manage synthetic sequences. This will contribute toward a broader effort to visualize the results of synthetic biology experiments in the computational design phase, after synthesis (via DNA re-sequencing), and to verify gene expression under various conditions (via RNA sequencing). We propose to store revisions of synthetic chromosome sequences in git (primarily github) repositories. The project would include the development of plugin components on both the server and client sides. The new extensions would provided a means of detection of branch and tag updates on the github repos and provide a means to select and retrieve the synthetic sequences from github. The backend part of the plugin would provide a means to manage multiple synthetic sequences and manipulate associated JBrowse-based datasets. This is a challenging and exciting project at the interface of computational and synthetic biology. You’ll have lots of guidance developing cool science tools that will have a relevant impact to the scientific community.<br />
**''Expected results:'' Your module will be exploited at large by a new breed of synthetic biologists.<br />
**''Knowledge prerequisites:'' Candidates should have some good experience with Javascript, HTML5 & CSS3. Experience with REST, Node.js, Dojo, and jQuery, or Github API would be a plus (you’ll be learning it all). If you think biology is cool and would like to learn a lot more about it, that’s a plus too. <br />
**''Skill level:'' Medium<br />
**''Mentors:'' Eric Yao, Lead JBrowse Developer<br />
<br />
*'''Project Idea 3: Lightweight chat plugin for the JBrowse genome browser'''<br />
**''Brief explanation:'' Increasingly, genome scientists collaborate remotely from multiple sites: at genome centers in academic institutions, from biotech companies, from clinical labs and (increasingly with the advent of portable genome sequencing) from field sites. This project idea is to develop a lightweight messaging/chat plugin for JBrowse using OAuth2 and the Faye pub/sub framework. Users will be able to see who else is currently browsing the genome (provided that they have set themselves as visible), to see where they are browsing, and to send and receive messages. A possible extension is to post comments on the genome. The general idea here is to make genomes (and their constituent objects, e.g. gene annotations) into “social objects”. This is in keeping with our vision of JBrowse as not just a tool for genomics, but for social genomics. The availability of thousands of JBrowse instances which could readily incorporate the plugin offers the possibility quick and deep adoption by the genomics community.<br />
**''Expected results:'' This module will enable a new way for bioengineers to share and socialize genomic information.<br />
**''Knowledge prerequisites:'' Javascript/HTML5/CSS3. NodeJS, Dojo a plus. Digging science, a plus. <br />
**''Skill level:'' Medium<br />
**''Mentors:'' Ian Holmes, Principal Investigator and founder of JBrowse</div>Ericiamhttp://gmod.org/wiki/GSOC_Project_Ideas_2016GSOC Project Ideas 20162016-02-17T22:12:22Z<p>Ericiam: Add JBrowse project ideas</p>
<hr />
<div>There are plenty of challenging and interesting project ideas this year. These projects include a broad set of skills, technologies and domains, such as GUIs, database integration and algorithms. <br />
<br />
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. <br />
<br />
*'''Project Idea Name'''<br />
**''Brief explanation:'' Brief description of the idea, including any relevant links, etc. <br />
**''Expected results:'' describe the outcome of the project idea.<br />
**''Knowledge prerequisites:'' programming language(s) to be used, plus any other particular computer science skills needed.<br />
**''Skill level:'' Basic, Medium or Advanced.<br />
**''Mentors:'' name + contact details of the lead mentor, name + contact details of backup mentor.<br />
<br />
<br />
Here is a list of the proposed project ideas for 2016:<br />
<br />
*'''Project Idea 1: Biological Graph Visualization'''<br />
**''Brief explanation:'' Tripal (http://tripal.info) is an open-source suite of Drupal modules that allows a scientific research community to more easily setup and manage a data repository for genomic, genetic and related biological data. It provides data pages, data mining tools and visualizations. Tripal is used or in development by over 25 different genome database websites, and is developed by an international group. A Tripal module currently exists for importing, searching and visualizing graph data that models the "network" of interactions of various components of a biological system. However, the module is not complete and requires improvements to the visualizations. The goal of this project would be to complete the remaining work for this module such that it can be shared with others.<br />
**''Expected results:'' Once completed, a Drupal module will freely available for Tripal-based sites to use on their own sites. Thus providing graph visualizations for complex biological systems.<br />
**''Knowledge prerequisites:'' PHP, Drupal, JavaScript, SQL.<br />
**''Skill level:'' Medium<br />
**''Mentors:'' Stephen Ficklin<br />
<br />
*'''Project Idea 2: Github-based revision control of synthetic chromosomes'''<br />
**''Brief explanation:'' JBrowse is a robust open-source genome visualization tool built around Javascript and HTML5. It has gained wide acceptance among biologists and bioinformatisist with thousands of active installations worldwide in genomic research. Synthetic biologists design DNA sequences that differ from their analogous sequences in natural organisms. As with code, the differences can be incremental or radical, and can be visualized using “diff”-like tools. And, also as with code, good revision control is fundamentally important. We propose to build module that enables biologists to manage synthetic sequences. This will contribute toward a broader effort to visualize the results of synthetic biology experiments in the computational design phase, after synthesis (via DNA re-sequencing), and to verify gene expression under various conditions (via RNA sequencing). We propose to store revisions of synthetic chromosome sequences in git (primarily github) repositories. The project would include the development of plugin components on both the server and client sides. The new client extensions would provided a means of detection of branch and tag updates on the github repos and provide a means to select and retrieve the synthetic sequences from github. The backend part of the plugin would provide a means to manage multiple synthetic sequences and manipulate associated JBrowse-based datasets. This is a challenging and exciting project at the interface of computational and synthetic biology. You’ll have lots of guidance developing cool science tools that will have a relevant impact to the scientific community.<br />
**''Expected results:'' Your module will be exploited at large by a new breed of synthetic biologists.<br />
**''Knowledge prerequisites:'' Candidates should have some good experience with Javascript, HTML5 & CSS3. Experience with REST, Node.js, Dojo, and jQuery, or Github API would be a plus (you’ll be learning it all). If you think biology is cool and would like to learn a lot more about it, that’s a plus too. <br />
**''Skill level:'' Medium<br />
**''Mentors:'' Eric Yao, Lead JBrowse Developer<br />
<br />
*'''Project Idea 3: Lightweight chat plugin for the JBrowse genome browser'''<br />
**''Brief explanation:'' Increasingly, genome scientists collaborate remotely from multiple sites: at genome centers in academic institutions, from biotech companies, from clinical labs and (increasingly with the advent of portable genome sequencing) from field sites. This project idea is to develop a lightweight messaging/chat plugin for JBrowse using OAuth2 and the Faye pub/sub framework. Users will be able to see who else is currently browsing the genome (provided that they have set themselves as visible), to see where they are browsing, and to send and receive messages. A possible extension is to post comments on the genome. The general idea here is to make genomes (and their constituent objects, e.g. gene annotations) into “social objects”. This is in keeping with our vision of JBrowse as not just a tool for genomics, but for social genomics. The availability of thousands of JBrowse instances which could readily incorporate the plugin offers the possibility quick and deep adoption by the genomics community.<br />
**''Expected results:'' This module will enable a new way for bioengineers to share and socialize genomic information.<br />
**''Knowledge prerequisites:'' Javascript/HTML5/CSS3. NodeJS, Dojo a plus. Digging science, a plus. <br />
**''Skill level:'' Medium<br />
**''Mentors:'' Ian Holmes, Principal Investigator and founder of JBrowse</div>Ericiamhttp://gmod.org/wiki/User:EriciamUser:Ericiam2015-04-24T18:30:21Z<p>Ericiam: </p>
<hr />
<div>Lead Developer on JBrowse, a Genome Browser at UC Berkeley, Institute of Quantitative Biosciences.<br />
http://jbrowse.org<br />
<br />
Technical Director and Chairman of Wonderfest, Bay Area Beacon of Science<br />
(a San Francisco Bay Area science lecture series)<br />
http://wonderfest.org<br />
http://facebook.com/wonderfest<br />
<br />
Eric is a senior full-stack web architect, software engineer and entrepreneur who is bio-curious and a general science enthusiast.<br />
He is so amazed that life is written in molecular soup and that creatures crawl out of the bowl.</div>Ericiamhttp://gmod.org/wiki/User:EriciamUser:Ericiam2015-04-24T18:29:39Z<p>Ericiam: </p>
<hr />
<div>Lead Developer on JBrowse, a Genome Browser at UC Berkeley, Institute of Quantitative Biosciences.<br />
<br />
Technical Director and Chairman of Wonderfest, Bay Area Beacon of Science<br />
(a San Francisco Bay Area science lecture series)<br />
http://wonderfest.org<br />
http://facebook.com/wonderfest<br />
<br />
Eric is a senior full-stack web architect, software engineer and entrepreneur who is bio-curious and a general science enthusiast.<br />
He is so amazed that life is written in molecular soup and that creatures crawl out of the bowl.</div>Ericiamhttp://gmod.org/wiki/User:EriciamUser:Ericiam2015-04-24T18:28:27Z<p>Ericiam: Lead Developer on JBrowse, a Genome Browser at UC Berkeley</p>
<hr />
<div>Lead Developer on JBrowse, a Genome Browser at UC Berkeley, Institute of Quantitative Biosciences.<br />
http://jbrowse.org/<br />
<br />
Technical Director and Chairman of Wonderfest, Bay Area Beacon of Science<br />
(a San Francisco Bay Area science lecture series)<br />
http://wonderfest.org<br />
http://facebook.com/wonderfest<br />
<br />
Eric is a senior full-stack web architect, software engineer and entrepreneur who is bio-curious and a general science enthusiast.<br />
He is so amazed that life is written in molecular soup and that creatures crawl out of the bowl.</div>Ericiamhttp://gmod.org/wiki/User:EriciamUser:Ericiam2015-04-24T18:26:40Z<p>Ericiam: </p>
<hr />
<div>Lead Developer on JBrowse, a Genome Browser at UC Berkeley, Institute of Quantitative Biosciences.<br />
<br />
Technical Director and Chairman of Wonderfest, Bay Area Beacon of Science<br />
(a San Francisco Bay Area science lecture series)<br />
http://wonderfest.org<br />
http://facebook.com/wonderfest<br />
<br />
Eric is a senior full-stack web architect, software engineer and entrepreneur who is bio-curious and a general science enthusiast.<br />
He is so amazed that life is written in molecular soup and that creatures crawl out of the bowl.</div>Ericiamhttp://gmod.org/wiki/User:EriciamUser:Ericiam2015-04-23T23:48:19Z<p>Ericiam: </p>
<hr />
<div>Lead Developer on JBrowse, a Genome Browser at UC Berkeley, Institute of Quantitative Biosciences.<br />
<br />
Technical Director and Chairman of Wonderfest, Bay Area Beacon of Science<br />
(a San Francisco Bay Area science lecture series)<br />
http://wonderfest.org<br />
http://facebook.com/wonderfest<br />
<br />
Eric is a senior full-stack web architect, software engineer and entrepreneur who is bio-curious and a general science enthusiast.<br />
He is so amazed that life is written in molecular soup and that creatures crawl out of the bowl.<br />
He also enjoys studying neuroscience and its cross section with politics and policy.<br />
Eric's greatest peeve is the influence of money in politics and government (aka crony capitalism) and is an activist towards ending it.</div>Ericiam