NRNB values feedback from the network biology community. Below is a collection of testimonials collected from collaborators, students and mentors when asked how their interaction with NRNB has impacted their involvement with the network biology community as well as their carreer opportunities and training. We have also collected and published profiles for some of our amazing students over the years.
“This milestone will shine on my CV forever.”
“The greatly appreciated point was communicating with my mentor. He shared all the knowledge with me to complete this project.”
“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.”
“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.”
“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.”
"It's not only a good opportunity to work with professional developers to improve the programming skills, but also a chance to learn biological knowledge and better understand the biological systems through meeting with those experienced tutors."
"I feel great to work with a group of enthusiastic biologists, engineers and developers on many interesting projects."
"That is the very valuable experience and it could be very helpful for either job hunting or applying gradate school. There are lots of people in this community know Cytoscape very well."
"I already published one paper and another one is in preparation. All of them are based on my GSoC projects with NRNB."
"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."
"Thanks to the participation and the projects done in Google Summer of Code with NRNB, I was selected for an internship at INRIA Paris and also did my Undegrad thesis there subsequently. The experience with NRNB helped improve my technical skills and gave me strong experience in professional software development."
"I participated in the Google Summer of Code after my first year of Undergraduate Studies. It was an amazing learning experience and introduced me to Open Source development. It helped me improve both my technical and interpersonal skills."
"Involvement in the GSOC with NRNB was all upside for me. In my search for a network visualization tool I found Cytoscape as the best alternative, but it lacked the capability to visualize dynamic graphs. Discussion with the Cytoscape community rapidly progressed into mentoring a GSOC project with an excellent applicant. Ultimately I gained the dynamic network visualization tool that I sought, along with experience as a mentor, experience in open-source development, and in gaining a number of valuable academic contacts. All good!"
"I have had great pleasure working on the NRNB training programs, and I can say that I've greatly benefited from them. Not only I was introduced to the Network Biology research community, but I also learnt many technical skills along the way. Currently, I'm participating for a last time as a student in NRNB GSoC, and after my upcoming graduation I am definitely interested in continuing my involvement with this great community. If it weren't for NRNB training programs, I would have never got in touch with the people I'm working on, nor with this amazing field of study."
"I made valuable academic contacts and also developed important software tools."
"Provided good initial contacts in the Network Biology community."
"It provided me with real world, hands on experience that allowed me to have just landed on a great job."
"Before NRNB I have had no contact whatsoever with the Network Biology research community. Now, I have written and published several pieces of code that are being used by biologists."
"It opened new career opportunities for me, and allowed me to get new work experiences. I was able to cite the experience in subsequent job interviews and it was very helpful to my career."
"The program exposed me to a new experience and allowed me to expand my knowledge in the field. By engaging me and challenging me, my mentors made me learn a great deal. The program was a big boost to my career advancement and it gave me the experience I needed to move towards my goals. As a student, the program allowed me to deepen my technical knowledge and let me go beyond the theory that I learn in my studies. My mentors were incredibly helpful and it was a remarkable learning experience."
"I was part of the Google Summer of Code program in collaboration with NRNB. I had the opportunity to learn and work with Mr.Augustin Luna (main mentor) and Dr. Martijn P. van Iersel (my secondary mentor). I had never been part of such a big project until I worked with NRNB. It was great to work on my plugin from scratch and integrating the things with PathVisio and working with Pathvisio's source code base. Lot of days I worked with my mentor Mr.Augustin way past our usual timings in the night and that was fun. Suddenly we would come up with a solution to a particular problem and this was very satiating."
"I had co-authored a paper along with my mentors for GSOC. This was a huge surprising bonus along with the other benefits of being a GSOC student of NRNB. This gave an edge to my grad-application when I applied to universities for my MS in Computer Science."
"It has had a great impact on my career and I learnt a lot during the period I worked with my mentor Mr. Augustin Luna. It was fun, very wonderful and and extremely productive experience. Working with XSLT and other related technologies in developing the plugin also helped me through my job in India."
"It certainly was a big boost for my career. I was told by my actual employer that one of the things that made my resume stand out was my experience from GSoC with NRNB."
"I simply had no involvement at all with the Network Biology research community prior to the NRNB training programs I took part in, and now I'm actually starting to work on a Master Thesis (in computer science) that will heavily involve Cytoscape and other NRNB tools."
"In my personal opinion, the 3 GSoC NRNB programs I took part in were hugely successful for my career. I did not only got involved with the Network Biology research community, but also with open source software development and a lot of techniques and tools that were previously unknown to me. I really hope these training programs continue, so that many more people can have the same opportunity that I did."
"I started graduate school the year after completing GSoC. My experiences during the summer of 2010 helped to prepare me for that endeavor. In particular, my graduate program requires all first year students to take a programming exam, and my experience with GSoC turned out to be a fantastic way to study for this exam."
"My direct line of research has drifted away from network biology since completing GSoC, however my experiences have enabled me to help/mentor others in my research group who do work directly on problems in network biology."
"I had absolutely fantastic mentors when I participated in GSoC in the summer of 2010. I believe they were a large reason why I feel that this program really helped to give me a leg up in both confidence and skill when I started graduate school."
"My experience gave me the coding and teamwork skills to succeed in a fast paced graduate program. It provided me with a solid base that I have since come to recognize as extremely valuable. It also helped to build critical connections within a larger community."
"The GSoC project allowed me to fully focus on programming for a couple of months in the beginning of my PhD project, and learn to know the relevant open source communities. This set the tone for my further PhD research and career (I am now applying network biology approaches to research to metabolic health research)."
"I learned how to develop real software that was both technically sound and biologically relevant. I also got to work with exceptional people from whom I was able to learn a great deal about the development of open source software projects and the importance of community, teamwork, and passion in the pursuit of developing great code. Overall this program significantly broadened my horizons, undoubtedly helped pave the way to grad school, and most importantly provided me with a great learning experience from which I continually benefit."
"This NRNB training program provided a great chance to me to improve my various kinds of skills. It helps build up my programming experience. Also, I could make my contribution to Biology reseach and open source community as well. I really appreciate the organizaiton giving me this opportunity!"
"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 GSoC."
"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 GSoC."
"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."
"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."
"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."
"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."
"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."
"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."
"It has given me an opportunity to gain hands on experience and learn, ultimately leading to a better profile which has helped me with my interview opportunities."
"I have read a lot of papers related to computational biology etc and have used those in my projects over the last two years. It feels great to have contributed and I hope to keep on doing this in future."
"I was personally intrigued by clusters and theirs applications, did a project related to those and data mining. NRNB gave me a platform to learn the applications of clustering in the field of biological networks and it turned out to be much more than I imagined. I have been learning a lot from the interactions with my mentor and i believe it has evolved my technical skills."
"NRNB gave me the first opportunity in the open source world. I have gained enormous amount of coding skills and this enhanced my path in professional career."
"Initially I had minute knowledge on Biology. Later, I learnt a bit of Bioinformatics. I did gain more knowledge on the visualization techniques used to analyse sequences. I was exposed to lot of Applications of Network and Graph theory."
"It was a great experience with NRNB. It blessed me with a great deal of opportunities to learn Bioinformatics,Computational Biology. I have acquired immense knowledge on System Biology and Graphical Notation (SBGN), SBML. I am well versed with the Graph and Network Theory at application level and lot of Visualization too."
"My coding skills have been improved. One of the main thing is, we get a chance to code from the scratch, which is a rare opportunity for a student. And our apps are used by many."
We have a backlog of success stories to highlight here as published student profiles. These students highlight the benefits of the GSoC experience in a professional career. If you are seeking talented network biology technology developers, then this is a great place to start!
"The program has been great experience for my students. They not only learned about open source community driven projects, but the work they did has contributed to their future research."
"Personally, I see great value in interacting with smart, young people from all around the world. I am optimistic that participating in NRNB training programs will benefit my own research group by giving it wider exposure and by building a community around the software.
"The program gave me a chance to work with students in projects of mutual interest and to develop my tools faster and more efficient."
"Great opportunity for developing mentoring and supervising skills as well as get my software tools developed."
"In Bioinformatics, there is always a lot more ideas floating around than people to code them. GSOC is great because it gets us the extra help we need, even if for a short while. For me at NIH, which has no regular students of an academic institution, it can sometimes be tricky to get summer students, especially good programmers; this helps out in that respect, as well. As a mentor, I see it as an opportunity to help students better understand the biological-sciences community, especially if they are coming from something like a computer science background, and the opportunity to go through the whole process of blank code window to an academic publication of that work, which I believe should greatly add to the whole experience and resume/CV."
"I developed two Cytoscape plugins AdvancedNetworkMerge and CyThesaurus in 2008 and 2009 as a GSoC student and has been maintaining these two plugins since then. By participating in the GSoC NRNB training program, I have learned tremendously about network biology and decided to build my research career in this area. After my Ph.D graduation in 2011, I joined one of the NRNB investigator -- Chris Sander's lab at Memorial Sloan-Kettering Cancer Center. My first project as a postdoc is a NRNB-supported project: integrating biological pathways / networks in the cBio Cancer Genomics Portal using CytoscapeWeb. In 2012, I became a GSoC mentor for NRNB, co-mentoring a student to develop a Cytoscape plugin Mondrian for retrieving, visualizing and analyzing cancer genomic data for Cytoscape networks."
"The GSoC NRNB training program opened a door to network biology for me. Before enrolled in the GSoC program, I did not know much about the field, but I was able to make my contribution by coding while learning as a student. Now I am able to use my expertise to train other students on network biology as a mentor. In summary, GSoC NRNB training program provided me with a great channel to not only learn from but also contribute to the community."
"During the first GSOC year, in 2007, we were actually developing WikiPathways as GSOC students. (My particular project was the history browser of WikiPathways) Now, WikiPathways a household name amongst biologists, with hundreds of citations and thousands of visits per month. NRNB has made that possible."
"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."
"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.
"Through the program I have got to know many people in the field around the world. NRNB has broadened my horizons."
"Helped me find talented graduate students."
"Both mentors and students involved in the programs are outstanding software developers dedicated to producing tools and software for network biology community."
"Help me initiate some important collaboration with others in the community."
"Through GSoC, I got familiar and envolved with the Network Biology research community and finally decided to join Chris Sander's lab as a postdoc to work in this area."
"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."
"The NRNB training program has given me a chance to be part of a global team of like-minded people, and to advance much further in the field of network biology, than what would have been possible in isolation."
"From my point of view, GSoC allows the open source community to engage people from all over the world to participate and be active. You get to know a lot of people, which will always help you in your future professional career. I learned a lot during the two years I participated in GSoC, not only in programming (although I learned a lot), but also how to interact with people over different media (email, video chat,...). Communication is really one of the most important tools that you have to learn because nowadays collaborations will always get bigger and more distant. It is not possible to meet in person every week, so you have to learn how to use the communication tools that you have at hand."
"2011 was an interesting challenge with a student who ended up abandoning the project at the midterm. It was actually helpful to get some experience in active management of a graduate student, even though the coding part of the project was not completed. The same project was continued in 2012, with me as a secondary mentor on the project. It was gratifying to make progress on the project the second time around!"
"Much of the code developed under the NRNB training programs was well aligned with problems from my own research agenda. Also, it enabled me to keep abreast of the latest software methodologies and tools. Most importantly, I established enduring professional relationships with the students I mentored. A number of them returned to the training program as mentors themselves."
"Again, very positively. I was co-author on a number of publications, which in turn enhanced my stature in the Network Biology community. Also, I was able to establish connections with leading network biology researchers by co-mentoring with them."
"It was very educational and useful for my future career. The program gave me the possibility to work in an open source project in the summer, get money for it and get to know lots of people that might be helpful in the future when I am looking for a job. It was an absolute great experience."
"We worked with great summer students and multiple software features and scientific publications resulted."
"I made valuable connections to the research community as a result of my participation in the mentorship in 2011 and 2012."
"It's been helpful to make connections with others in the Cytoscape plug-in development community. I made several connections with individuals involved in the network biology community, and this lead to additional work for me on a collaboration on a Cytoscape plugin for network permutation, and on a project to add a few features to GenMAPP-CS."
"NRNB training programs have been highly valuable to our research. We have been involved in mentoring nine GSoC students since 2007. The majority of the projects have resulted in useful new features in Cytoscape, Cytoscape Web and new plugins, two of which have been published."
"I was a mentor for a number of years on the Google Summer of Code program. I co-mentored projects in the area of graph layout, network search, and visual data overlay. I think that the program provides excellent opportunities for open source software organizations to build enduring working relationships with young, talented developers and researchers. For an applied researcher like myself, it provided excellent opportunities to see research issues from multiple perspectives -- from that of the talented young developers to that of the researchers of stature who were my co-mentors. It helped me to keep my own skills fresh and relevant."
"Thanks to NRNB training programs, I have first become familiar with the software tools NRNB has been providing, then with the people behind those tools, and finally with the research projects being conducted as part of NRNB."
"NRNB promotes a really healthy student-mentor relationship and I believe this is one of the most important aspects of the training programs. It is fairly easy to get a question answered or a problem solved by someone else's help on the mailing lists, there is always updated training material on the web site--which really helps with the kickstart--and I do appreciate the successful outreach programs that helped me get involved with NRNB and encourage the spread the word. That is definitely why I became a mentor for the GSoC'12 program! Finally here is a great anecdote regarding my involvement in the GSoC program: In 2008 when I was a undergraduate student in Turkey, Jianjiong Gao (then a graduate student in China) and I have worked together on closely related Cytoscape projects during the Google Summer of Code program. Now, in 2012, we are both working with Chris Sander, an NRNB PI, and we have been working side-by-side for almost two years now at the same lab (he as a post-doc and I as a graduate student). We have even co-mentored a GSoC student this year and will hopefully do the same for the following year's program."
"The first time I was involved in the GSoC program, I was an undergraduate (studying Molecular Biology and Genetics) and I had been mainly doing wet-lab experiments as part of my training program (Bogazici University, Turkey). I always had an interest in Bioinformatics and Computational Biology, but never had experience in working in a well-defined project. In 2008, as GSoC student, I had the opportunity to work on a well-defined project for three-months, and this definitely helped me make my mind up to apply graduate school and pursue my education in Computational Biology. During the graduate school applications, being part of the program really helped in proving my experience to the graduate school committee (especially during the interviews). I am now part of the Tri-Institutional Training Program in Computational Biology and Medicine and I believe NRNB & GSoC has an invaluable contribution in this."
"Participating as mentor in GSoC projects Cytoscape plugin development, and joining the Cytoscape retreat, helped me to get more familiar with the Cytoscape development community and network biology research community in general."
"Participating in the GSoC program both as student and mentor, was each year a very inspiring experience where I got to know other researchers involved in the same research field, worked with very motivated students, and where despite the short duration of each project, we together made great and lasting contributions to the open source community."
"Helped us organize an idea into a project with concrete deadlines and goals. This has motivated us to push development, write grants, and work towards publications."
"It has helped our lab build working relationships with a Cytoscape and WikiPathways programmer, leading to two grant submissions and hopefully publications soon."
"We enjoyed the program, particularly when the students developed a project directly related to our project. In the second year, the fit was less ideal (expertise and project mesh), but we still learned a great deal from the process and from the perspectives of the student's research. Next year we hope to propose two projects that will merge and generalize the efforts of the first two years."
"I was introduced to the exciting field of network biology through collaboration with Rintaro Saito and Trey Ideker at UCSD. Within the framework of the San Diego Center for Systems Biology (SDCSB), we approached the mechanistic description of autophagy in human cells from a network perspective. For these projects the input by Drs Saito and Ideker was of utmost importance: we developed an autophagy focused interaction network and analyzed this by standard and novel bioinformatic tool sets; other projects within our lab also greatly benefitted from this collaboration in that we used network tools to describe yeast pathways. Several publications benefitted from this collaboration; our current and future goals and aims were significantly shaped by the interaction with Drs Ideker and Saito. We highly appreciate their influential contribution."
"Our work with the Bader lab, has and continues to be an innovation driver in our genomic analysis of spontaneous lymphocytic leukemia in mouse models and patient samples. In addition Bader's tools are helping us to design approaches to analyze highly dimersional phospho flow cytometry analysis of basal signaling networks in leukemic cells, and the to profile specific patient tumor responses to new small molecule inhibitors."
"NRNB was instrumental in collaborating with my lab group on the studying the protein architecture of human secretory vesicles, to organize proteomics data into functional networks regulating neurotransmitter secretory functions. Dr. Trey Ideker, lead collaborator of NRNB, provided expertise and had his lab colleagues assist my lab in network analyses of our data. The analyses was essential for understanding predicted biological functions, that were supported experimentally in the study. This wonderful collaboration resulted in a joint publication. We plan to continue collaborating with NRNB and, thus, renewal of the NRNB program is essential to understanding networks of pathways in biological systems, and especially in human diseases."
"I received support from the T. Ideker group with the construction of a combined genetic and physical interaction network using the PanGIA Cytoscape plugin they had developed. The analysis has given us unique insights into protein complexes and cellular machines undergoing regulation in response to stress conditions. The Cytoscape developer group was then kind enough to also port the PanGIA plugin for the new Cytoscape 3.0 version, whcih was extremely helpful for us."
"The collaboration developed a new useful tool for network ontology analysis."
"We received help learning about some of the features of cytoscape. We now routinely use this tool through RCytoscape in the lab."
"The NRNB group was extremely helpful in getting us thinking about network analyses and their potential for advancing our research in microbial pathogenesis and gastrointestinal diseases. We are now in the process of formulating specific projects and grant ideas for long-term pursuit of these new opportunities."
"Over the past years, my collaboration with the NRNB team has not only been key in maintaining the Cytoscape plugin BiNGO, which I developed back in 2005 and which is to this day one of the most popular Cytoscape plugins, but more recently also resulted in the development of another network biology plugin, PiNGO, which was published in Bioinformatics in 2011. Overall, collaboration with NRNB staff has always been extremely smooth and productive."
"Our collaboration successfully applied a network tool that predicted previously unrecognized protein-protein interactions. We biochemically confirmed these interactions in a publication in collaboration with an NRNB group."
"Great interactions with Bader. Led to a nice publication and the continuing development of new ways to model and analyze cell-cell interaction networks."
"I worked with NRNB to develop an app NOA for Cytoscape 2.8. It is a novel ontology-based network analysis tool. With Dr. Pico's help, we saved a lot of time for developing this app. We also published a paper Network-Ontology Visualization and Analysis at Bioinformatics in 2013 together. Besides this published work, we are working on porting this app with another two apps to Cytoscape 3.0. Since Cytoscape 3.0 is a new platform for us, we got a lot of information from Dr. Pico's group, and it will be very helpful for us to port app to version 3.0 in a short time."