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Describe your organization.

Machines that build machines = Biology.  Networks are how biology communicates and computes.  BEL (Biological Expression Language) captures and communicates biological networks for both Biologists and Computational Scientists in an easy to use and powerful format.  

OpenBEL is an open source and open community project providing BEL (Biological Expression Language) and a set of tools to process/store biological knowledge.  The community was formed in earnest in May of 2012.

OpenBEL is collaborative project under the sponsorship of the Linux foundation.

See What is OpenBEL?.


Why is your organization applying to participate in Google Summer of Code 2014?

OpenBEL has always strived to include more community members interested in modelling biology.  A mentorship program provides a chance for excited students to understand and be a part of the community.  Mentors in turn will also learn from the students and promote a relationship for continuing participation in the community.

Additionally we have many new project ideas that are meaningful and relate to current technology trends (e.g. semantic web, web visualization, web interfaces).


What do you hope to gain by participating?

We hope to find excited students who want to be a part of the OpenBEL community.  OpenBEL will benefit from the student's work and the whole community will benefit from their experience.  Additionally we hope participating students will publicly share their progress and enthusiasm for their work.


Has your organization participated in past Google Summer of Codes?

No, this is the first GSoC after OpenBEL became official.


If you answered “yes” to the question above, please summarize your involvement and the successes and challenges of your participation. Please also list your pass/fail rate for each year.



If your organization has not previously participated in Google Summer of Code, have you applied in the past? If so, for what year(s)?

No. This is our first participating year.


What Open Source Initiative approved license(s) does your project use?

Apache License, Version 2.0 ( )


What is the URL for your Ideas list? **This is the most important part of your proposal. Please make sure we can access it and it is complete when you submit this proposal. “Placeholder” or inaccessible ideas pages will be grounds for an automatic rejection for participation in Google Summer of Code 2014.**

See OpenBEL Project Ideas.


What is the main development mailing list for your organization?

Google group: openbel-discuss


Subscribe email: with subject "subscribe".


What is the main IRC channel for your organization?

#openbel on freenode


Who will be your backup organization administrator?

William Hayes


What criteria did you use to select the mentors? Please be as specific as possible.

The mentors were selected based on active participation in the OpenBEL community.  The four mentors selected have actively participated in discussion, design, and development of OpenBEL for about two years.


What is your plan for dealing with disappearing students? Please be as specific as possible.

Firstly we shall minimize the risk that a student disappears.  We will:

  • Select students excited in participating with and contributing to OpenBEL
  • Engage with the students immediately after selection
  • Understand each student's work conditions (e.g. weather, internet access stability, work hours)
  • Provide documentation on our wiki to help them get started in the community, the code, and their project
  • Promote a cordial and responsive relationship between the students and mentors

If a student were to disappear from a project we will (in sequence):

  • Understand why the student is disconnected or disengaged
  • Try to substitute the student if early in the project
  • Fail the student


What is your plan for dealing with disappearing mentors? Please be as specific as possible.

Firstly we shall minimize the risk that a mentor disappears.  We will:

  • Select mentors who are experienced and actively participate in the OpenBEL community and projects
  • Set expectations and guidelines early for mentor participation
  • Org Admin will continually check in with mentors on the student/mentor relationship

If a mentor disappears from a project we will (in sequence):

  • Understand why the mentor is disconnected or disengaged
  • Assign a backup mentor if necessary


What steps will you take to encourage students to interact with your project's community before, during and after the program?

Before the program starts we will:

  • Provide information on communication channels (google groups, irc channel)
  • Provide documentation on the wiki that helps navigating our resources and projects
  • Have the mentors (+Org Admin) talk face-to-face with the students to establish a more personal relationship
  • Provide some small tasks that the motivated student could take on to better understand their project

During the program we will:

  • Provide feedback and check in periodically
  • Give direction if a student is stuck or has questions
  • Encourage open participation while the students work on their project (e.g. blog, mailing list discussions).

After the program (post evaluations) we will:

  • Understand where their interests and community goals intersect.
  • Encourage further development of their project.
  • Engage the student for further participation in the OpenBEL community.


Are you a new organization who has a Googler or other organization to vouch for you? If so, please list their name(s) here.



Are you an established or larger organization who would like to vouch for a new organization applying this year? If so, please list their name(s) here.


What will you do to encourage that your accepted students stick with the project after Google Summer of Code concludes?
  • Highlight the project success thus far and next steps
  • Continue to engage with the student through the OpenBEL community
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