GSoC and NRNB Academy Reports

We have participated in the GSoC program since 2007, and in addition to testimonials and yearly projects listings and success rates, we also produce a yearly report summarizing the projects and program.

2016 Report

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We were so excited to be a part of Google Summer of Code again after a year off! We pulled together over 50 project ideas and dozens of eager mentors to develop open source code for network biology research. We selected 15 proposals that brought together well-matched students, mentors and project ideas.

All 15 students passed their midterm and final evaluations, resulting in a wide range of (mostly) production-ready code, covering algorithm, UI, importer and converter development for both web and desktop for Cytoscape , cytoscape.js, SBML, SBGN , cBioPortal, Cell Designer, GraphSpace and more.

We are proud of the technical accomplishments and productivity of our students, and we are also proud of the many important aspects of diversity our students represent in the GSoC program, including geographical, gender and academic. Here are some numbers and facts about our 15 students compared to overall GSoC 2016 student stats in parentheses:

  • 9 different countries, including 1 (of 2) from Croatia, 1 (of 3) from Armenia and 2 (of 12) from Turkey
  • 20% female (compared to 12% overall)
  • Only 67% Computer Science (compared to 78% overall), including PhD students in Biological Oceanography and Medical Biochemistry & Biotechnology, an MS student in Bioinformatics, and a pre-med undergraduate.

Here are some quotes and blogs from our students this year. If you are considering applying as student (or mentor) next year, then read these for inspiration!

“My mentor team were great! They give me all the support I needed, but let me enough freedom to experiment with my own ideas. I would like to keep in touch with the team and to continue contributing.”

“I had the opportunity to learn and practice JavaScript with a very interesting project and having a mentor available was great for getting help when needed. The program seemed extremely well run and I would strongly recommend it to anyone interested.”

“Working in an NRNB [GSoC] training program helped to strengthen my resume and introduced me to the idea of combining a career in medicine with computer-based research.”

“I love the friendly atmosphere and the way the team works together. From the very beginning I felled well integrated in the group. It was pure fun to work together on the same project and to see how it's grown over the time. I could only recommend everybody to try out the NRNB training program.”

“The greatly appreciated point was communicating with my mentor. He shared all the knowledge with me to complete this project.”

“This milestone will shine on my CV forever.”

Some of our student blogs:

  • Hovakim Grabski – "Java support for Deviser, a code generation system for SBML libraries"
  • Kaito Ii – "Interconvertible Layout software for CellDesigner"
  • Roman Schulte – "Offline SBML validation in the Java-based JSBML library"
  • Mridul Seth – "Import graphs in multiple formats and Cytoscape files into GraphSpace"

2015 Report

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Our first venture into hosting our own summer mentoring program, the NRNB Academy Summer Session 2015, was a success! We mentored four students in network biology, open source software development while maintaining momentum with our development and mentor community for future summers. The students and mentors in this summer’s program completed 4 projects:

  • New features to CentiScaPe app for Cytoscape, by Sakshi Pratap.

    CentiScaPe is a popular app for Cytoscape 3 for extensive graph analysis. This was a very successful project, with many new features added. Both mentor and student are excited to continue Cytoscape development year-round and plan to participate in participate in future GSoC summer programs.

  • Porting support for SBML model import and work in Cytoscape, by Matthias König.

    This app, which provides SBML import and functionality to Cytoscape was successfully completed and submitted to app store at the end of this summer, and already has 493 downloads! A publication is in the works for this project as well.

  • SBGNViz.js: Cytoscape.js visualization of SBGN-ML diagrams, by Metin Can Siper.

    This project builds upon the cytoscape.js library to provide support for SBGN process description notation. Some of the constributions made to this project includes bug fixes, adding gui options, integrating a new cose layout, and releasing version 2.4.2.

  • Adding PCA to clusterMaker2, by Vijay Dhameliya.

    This project adds principle component analysis to the successful clusterMaker2 app, which provides over a dozen cluster algorithms and interactive heatmap visualization.

Here are some testimonials from this summer’s students and mentors:

“It improved my project managing skills. Especially the necessary skills for collaborative bioinformatics projects.”

“I had a very good experience with the NRNB. It provided the opportunity to work focused on a project for a limited amount of time. It allowed to bridge a funding period and realize a long hold idea into a software app.”

“It has been great. Beside improving my technical skills, it has increased my interest in visual analytics based application development and it is a field I am exploring more during my Masters."

“It was a great experience to be involved with the academy. I learned a lot about how graph algorithms and visualization can help in the research of bioinformatics. It was great to be mentored and improve.”

“It is an excellent experience to guide external students. This experience is also very helpful as part of my personal CV. Furthermore, since I had suggested the programing project, it is great that it was accepted and that I can now write this in my CV. Actually, it would be very nice if students and mentors could get some kind of "diploma" at the end for having this successfully conducted.”

“Both mentors and students involved in the programs are outstanding software developers dedicated to producing tools and software for network biology community.”

“This program was a great way to get in touch with other people from NRNB and I hope this will be continued with the next Google Summer of Code.”

“Helped me find talented graduate students. Help me initiate some important collaboration with others in the community.”

“The program was very similar to the Google Summer of Code. The interaction with students was very good, the evaluation and time line was very clear. Overall, an excellent program.”

2014 Report

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2014 (17/18 passing students, 94%)

Abhiraj Tomar - University of Southern California, Los Angeles, CA, USA
Implementation of new clustering techniques into Cytoscape
Mentored by Scooter Morris
Adam Shaw - University of Chicago, Chicago, IL, USA
Hierarchical Models in Segway
Mentored by Michael Hoffman
Alex Crits-Christoph - Johns Hopkins University, Baltimore, MD, USA
Developing An Interface For The Cancer Network Altering Variant Database
Mentored by Mohamed Helmy
Arman Aksoy - Memorial Sloan-Kettering Cancer Center, New York, NY, USA
Pathway Database Converters for the Expansion of Pathway Commons
Mentored by Augustin Luna
Truhin Alexandr - Technical University of Moldova, Chisinau, Moldova
Pathvisiojs Diff Viewer
Mentored by Anders Riutta
Shaik Faizaan - Birla Institute of Technology and Sciences, Pilani, India
Porting Interference App to Cytoscape 3
Mentored by Giovanni Scardoni
Rohan Saxena - Birla Institute of Technology and Sciences, Pilani, India
PathVisio Plugin to Load Additional Information about Data Nodes
Mentored by Martina Kutmon
Ankit Agarwal - Manipal University, Manipal, India
Virtual Cell iPhone App Enhancements
Mentored by Jim Schaff
Gerardo Huck - National University of Rosario, Rosario, Argentina
Graph Analysis Algorithms for Cytoscape.js
Mentored by Max Franz
Jonathan Melius - University of Maastricht, Maastricht, The Netherlands
Connect PathVisio and WikiPathways to Expression Atlas
Mentored by Lars Eijssen
Kirtan Dave - Sardar Patel University, Vallabh Vidyanagar, India
New Features for Interference App
Mentored by Cristian Munteanu
Lilit Nersisyan - National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia
PSFC: a Cytoscape app for calculating pathway signal flows
Mentored by Graham Johnson
Jimmy Morzaria - Birla Institute of Technology and Sciences, Pilani, India
Network Analysis Enhancements
Mentored by Jason Montojo
Niranjan Padmanabhan - McGill University, Montreal, Canada
ADAM Variation Services and Visualizations for Cytoscape 3 Variation App
Mentored by Michael Heuer
Sakshi Pratap - Birla Institute of Technology and Sciences, Pilani, India
Porting Pesca App to Cytoscape 3 with new features
Mentored by Giovanni Scardoni
Srikanth Bezawada - Birla Institute of Technology and Sciences, Pilani, India
Implementing TieDIE algorithm as a Cytoscape App
Mentored by Evan Paull

2013 Report

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As the National Resource for Network Biology, we are used to working with scaling networks of complex interactions, but there's nothing quite like the connections made through Google Summer of Code! This season we connected 26 of our mentors with 14 students from 9 countries over 4 continents. But the interactions go deeper than that. This was our 7th year participating in GSoC and we had students returning from prior years for another round of the program along with some past students who served as newly minted mentors themselves this year. And the output of these projects is soon to be in the hands of thousands of researchers studying the role of network interactions in biology and medicine.

We also experienced a tragic loss in our community this summer with the passing of Allan Kuchinsky, a champion of open source, network biology and GSoC. In his honor, we put together the Allan Kuchinsky Student Award and presented it to three of our GSoC students from this summer whose projects exemplified the principles of data visualization and good user-centered design that Allan was so passionate about. Congratulations and thanks to these excellent students!

Finally, here are some great quotes from some of our GSoC students this year. If you're considering applying next year -- the 10th year of GSoC! -- then these inspiring words should convince you.

"I've taken part in GSoC 4 times as a student working on network visualization techniques for Cytoscape and Cytoscape.js. Over those occasions, I was lucky enough to work with great people from all over the world (Hungary, USA, Canada, Turkey), and develop key abilities that will be really helpful in my professional future." - Gerardo Huck (Argentina) [github]

"My project ended up with adding tests, squashing git commits and making a pull request into main repository. Right after doing that I felt like I leveled up. The most important thing besides gathered experience is the fact that I did something tangible and useful." - Truhin Alexandr (Republic of Moldova) [github] [blog]

"These unbelievable life changing four months came to an end on 27th Sept when I completed final evaluations of GSoC. Things I learned as a part of GSoC: determination, collaboration with mentor and friends, and patience to read articles and documentation. I obviously will contribute to Cytoscape in future. In short, thanks to all the people involved in making GSoC 2013 a wonderful experience." - Shaik Faizaan (India) [github]

"This year's Google Summer of Code was quite an amazing and adventurous journey. It was very exciting and was very challenging. ...I learned a lot during this brief term of GSOC. I was hit with several roadblocks during the project but successfully solved them and made it to the end." - Sri Harsha P (India) [github] [blog]

Thanks to all the NRNB mentors and students, to all the other mentoring organizations, and a big thanks to the GSoC organizers. You have transformed how we work with students and new developers, and have catalyzed a lot of great code. See you next year!

- By Alexander Pico

2012 Report

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This year is the sixth year that Dr. Pico has coordinated the collective GSoC effort involving Cytoscape; this is the second year we’ve participated under the new banner of “NRNB”. Through the GSoC program we not only recruit new developers, but we are also significantly promoting NRNB as an open source-friendly organization, putting us in an exclusive list of ~175 organizations selected from around the world by Google to participate. Dr. Pico attends the annual GSoC Mentors Summit with other NRNB mentors to further engage the open source development community. In terms of collaborations, GSoC brings in new potential collaborators who want to participate as mentors in addition to the 40-60 student applicants. This year we coordinated 36 mentors (10 with NRNB funding), thus leveraging the effort of 26 additional developers from the open source communities surrounding NRNB-related tools. And through the GSoC program we received over 60 student applications this year. From these we’ve selected 16 students to mentor on Cytoscape and NRNB-related projects. The projects range from core Cytoscape 3.0, to Cytoscape 3.0 apps, to GeneMANIA and MedSavant, to PathVisio and WikiPathways, to the cBio Cancer Genomics Portal, but the majority of the projects are Cytoscape 3.0 related.

2012 (16/16 passing students, 100%)

Anwesha Dutta - University of Maastricht, Maastricht, The Netherlands
Extend PathVisio with a plugin to create , modify and visualize data on biological pathways from scripting languages
Mentored by Martina Kutmon
Chao Zhang - University of Missouri, Columbia, Missouri
Ontology-based Network Visualization and Analysis
Mentored by Alexander Pico
David Shih - University of Toronto, Toronto, Canada
Porting HOPACH cluster algorithm into clusterMaker
Mentored by Scooter Morris
Dazhi Jiao - Indiana University, Bloomington, IN, USA
Cytoscape Plugin for importing cancer genomic data and drug-target interaction data from cBio Cancer Genomic Portal
Mentored by Arman Aksoy
Istemi Bahceci - Bilkent University, Ankara, Turkey
SBGN-Complaint Views for Cancer Genomics Networks
Mentored by Ugur Dogrusoz
Jake Fried - University of Maryland, College Park, MD, USA
Understanding Complex Pathways using User Data and Web Services in PathVisio
Mentored by Augustin Luna
Khushi Chachcha - University of British Columbia, Vancouver Canada
GeneMANIA plugin for MedSavant
Mentored by Marc Fiume
Michael Kirby - University of California, San Diego, CA, USA
A Direct Interface Between R and Cytoscape
Mentored by Mike Smoot
Neil Dhruva - Birla Institute of Technology and Science, Pilani, India
Data summary of tables in Cytoscape
Mentored by Samad Lotia
Praveen Kumar - Jawaharlal Nehru Technological University, Hyderabad, India
Pathway Comparison in PathVisio
Mentored by Martina Kutmon
Rianne Fijten - University of Maastricht, Maastricht, The Netherlands
Plugin for metabolite information in Pathvisio
Mentored by Egon Willighagen
Ritisha Laungani - Birla Institute of Technology and Science, Pilani, India
Interactive path explorer through networks and biological pathways for Cytoscape
Mentored by Alexander Pico
Sabina Sara Pfister - University of Zurich, Zurich, Switzerland
Loading and visualization of dynamical networks in Cytoscape 3.0
Mentored by John Brown
Sinan Sonlu - Bilkent University, Ankara, Turkey
Layout Algorithms for New Cytoscape Web
Mentored by Ugur Dogrusoz
Yigang Zhou - Wuhan University, Wuhan, China
Visualizing Semantic Data Landscapes with Cytoscape 3.0
Mentored by Andra Waagmeester
Yue Dong - University of Toronto, Toronto, Canada
Cytoscape App Manager, Cytoscape Web WebGL Renderer and Layouts, Presentation API Testing
Mentored by Jason Montojo

2011 Report

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2011 (8/10 passing students, 80%)

Chao Zhang - University of Missouri, Columbia, MO, USA
GOLayout: Network partitioning and layout driven by GO ontology
Mentored by Alexander Pico
Martina Kutmon - University of Maastricht, Maastricht, The Netherlands
New PathVisio Plug-in Manager
Mentored by Martijn van Iersel
Marek Zaluski - Concordia University, Montreal, Canada
HTML5 prototype for Cytoscape Web
Mentored by Christian Lopes
Gerardo Huck - National University of Rosario, Rosario, Argentina
Connecting Cytoscape with igraph
Mentored by Gang Su
Avinash Thummala - IIIT-H, Hyderabad, India
A Cytoscape build with a fused (Annotation + Basic) editor based on an improved CyNetworkView with Neo4j interoperability
Mentored by Scooter Morris
Andrew Brook - University of Toronto, Toronto, Canada
Integrate Pathway Visualization and Analysis into Savant
Mentored by Marc Fiume
Yue Dong - University of Toronto, Toronto, Canada
Cytoscape Web - HTML5 Prototype
Mentored by Jason Montojo
Kumar Chandan - Keshav Memorial Institute of Technology (KMIT), Hyderabad, India
Real-time Validation Framework for Pathvisio
Mentored by Augustin Luna

2010 Report

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The GenMAPP organization’s efforts focus on building software tools to analyze and visualize biological data. We joined forces with Cytoscape, WikiPathways, PathVisio and Reactome for this year's Google Summer of Code to offer students a unique opportunity to work at the intersection of biology and computing. This was our 4th year participating in the program and we reached some new milestones. We mentored 10 excellent students (more than any prior year) with a 100% success rate. We integrated and released more code from this summer’s harvest than in prior years. And most importantly, we continued to expand our development community, as many of this year’s students are enthusiastic about continuing to work with us beyond the summer. Our projects this year covered a broad range of topics:

As part of the open source experience, we invite our Google Summer of Code students to our annual Cytoscape Retreat. This is a great way to engage students in both our development and user communities. One student pointed out a truism that is rediscovered from time to time in our digital age, “face-to-face meetings turn out to be very efficient.” Here are some other gems of reflection and advice from our students this year:

“The most rewarding part was when I was told that I should merge my changes back from my branch into the trunk"

“It has been the chance to meet and interact with wonderful people from various parts of the world, be it virtual or physical. I had a chance to physically meet another graduate student from my university and a professor from USA due to Google Summer of Code.”

“They opened up my perspective about a lot of things — how the industry looks like, where people with similar skill domain as me put themselves in the society, how important the projects I am involved in are, and other subjects unimaginable if I were to not join Google Summer of Code.”

“Got a taste of open-source development which is just amazing and I would like to keep attached with this project even after this GSOC ends.”

“This program is a great initiative, I loved the amount of exposure the participating students get and it definitely is one of the most exciting summers someone can ever get.”

“The most rewarding part is to be able to go to the cytoscape retreat. It is absolutely helpful to the project, and helpful to get to know the mentors and others.”

“Be the best user of the software. If you are the best user, you write and participate [in] the software project spontaneously.”

“At the beginning of the summer, I really had my doubts on whether or not I had gotten in too far over my head. So I very much enjoy being able to look back at what I was able to accomplish and realize that I was able to supersede my original expectations for myself.”

“Don’t be afraid to ask questions. Your mentors are an amazing source of information, and they are really interested in helping you in any way possible.”

“Be cool.”

- By Alexander Pico

2009 Report

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This was GenMAPP’s third consecutive year participating in GSoC and it was by far the most productive. As an organization we are continuing to learn how to be better mentors and the students continue to step up.

Our projects this summer covered three different projects: Cytoscape, GenMAPP-CS and WikiPathways, each working at the interface of biology and computer science. It takes a special type of student to succeed in this field and we found 9 of them this summer! Here is a brief description of the range of topics we covered:

  • Processing-based graphics renderer
  • Data mining interfaces
  • Animation tool using frame interpolation
  • Pathway model merging and visualization
  • Identifier mapping solutions
  • GPU utilization for graph layout
  • Phylogenetic tree visualization
  • Ontology-based categorization of pathways
  • Pathway exchange formats
In addition to the great code we produced, the GSoC experience is about building open source communities. We have had the great fortune of retaining most of our GSoC students from previous years, many of whom come back as mentors! And this year I have no doubt that we’ve significantly added to our ranks. But don’t take my word for it!

“Overall, this is the most productive summer I ever had. It increased my confidence as a developer and as a person that I can actually pull off a project like this and interact with awesome people like you. I also become a part of a growing community and hope to help it grow further.”

"There aren't many opportunities for computational biology enthusiasts to make a difference in the field while still in school. GSOC at GenMAPP/Cytoscape was one such gem of an opportunity that illustrated exactly why writing software for biological research is benefited by a background in biology. The experience I have gained here is definitely irreplaceable. The fundamentals of open-source programming and the rhythm associated with regular coding and problem solving helped nourish an intellectual side of me that I will not forget in a hurry. This is definitely not the last time you will see me."

“This was the first time I took part into either GSoC or an Open Source project, and it was also one of the most exciting things I've ever done! This project gave me the chance to spend ~3 months learning lot of new things, having fun, doing something for the community and even getting pay for that! That's an amazing combination! …I will remain as an active participant of the Cytoscape community beyond the official end of GSoC 2009!”

“It was definitely a very good learning experience for me. …But I have some unfinished works… So I'll continue this project after GSoC, and be help to drive Cytoscape 3 development.”

“It was the first time that I worked with an open source community and it was really a great experience. I am very thankful to Google and GenMAPP for providing me this great opportunity. I would like to thank [my mentors] for their excellent support during the summer. Looking forward to working with you again.”

“It was a GREAT experience to work with GenMAPP during GSoC 2009!!! The administrators and mentors were very helpful during bounding and coding periods. Whenever I had problems they were always responsive and offered me help in time. Under their guidance, I've improved my programming and communication skill, and learned how to work within a group. I would like to express my gratitude to all my mentors in GenMAPP. If I can participate in GSoC next summer, I would like to work with GenMAPP again:)“

2008 Report

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We were very fortunate to have 3 of our 4 students from last year participate as mentors this year. Our broader recruitment of mentors in general and their contributions to our Ideas Page, allowed us to take on 9 students this year. Though we lost one at the very beginning of the Summer, the other 8 were strong applicants. We assigned 2-3 mentors per student (a practice I highly recommend) and commenced with bonding.

By mid-term, we already knew we had some work to do for next year. The evaluations by our students all pointed to the fact that we have a dearth of tutorial and “starter” materials for developers. While I guess we already knew that, the feedback may help to prioritize the work (Google Summer of Documentation, anyone?). Here are some other paraphrased nuggets of wisdom from our students:

  • Get involved and interact with the community as early on as possible (e.g., even before applying).
  • Communicating is often more important than writing code.
  • Provide channels for your GSoC students to communicate with each other.
  • Organizations should try to get people together in person, via a retreat, party or any excuse.

On this last point of gathering for some face-to-face time, we serendipitously planned our annual Cytoscape Retreat during the Summer this year. The benefit to our GSoC students and the increased motivation on the projects was spectacular. In other isolated cases, students overlapped geographically with mentors allowing for in person meetings, but the effect of bringing the larger group together and having the students interact was multiplicative.

A final glance at our end-of-term evaluations bolsters our sense of success and pride for our students: 8 out of 8 said they were going to continue working on their projects and with our organization. Yay!

2007 Report

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2007 (4/4 passing students, 100%)

Nikolic Aleksandar - University of Nis, Leskovac, Serbia
Graph layout library for Cytoscape
Mentored by Mike Smoot
Maital Ashkenazi - The Hebrew University, Jerusalum, Israel
Maital's blog entry about GSoC 2007
Enhanced search strategy in Cytoscape
Mentored by David States
Thomas Kelder - University of Maastricht, Maastricht, The Netherlands
Pathway editor for wikipathways
Mentored by Kristina Hanspers
Martijn van Iersel - University of Maastricht, Maastricht, The Netherlands
Visual history of pathway modifications
Mentored by Alexander Pico