After long time analyzing bioinformatics scientist behaviour, I finally figured out that no real effort is done to let computational biologist interact with each other, a simple observation can serve as a proof of my statement, there is no collaborative platform for sharing source code dedicated to bioinformatics, a simple but very important issue that could help scientists develop even 10 times faster, by providing "patterns" of what other scientist have already done.
Developers and communities of Bio* projects behave like a closed group in regards to others, a considerable effort and useful tool such as mailing lists certainly provides communities with useful help, but there is no real effort to publish solved source code after they are examined and corrected by experienced programmers, resulting to make developers and mailing list admin to answer sometimes the same problem twice and even much more. (I see sometimes list admins refering to a previous post or thread, that's a good proof)
Starting from that point, I tried to see if such initiative was already taken, none of bioconductor, bioperl, biojava, biopython communities have a resources website storing high quality source codes and case study codes (of course I am not talking about all demo codes, cook books, or illustrations that constitute the developers starter kits to let scientist adapt a Bio* project to their need)
As I used to work with bioperl, biojava especially and now working with Bioconductor and R since I switched my research to the epigenomics side, I asked some people in the BioC list if they are willing to see a collaborative platform for people wanting to share their source codes, and the result was very appealing :
How can you describe your R/Bioconductor learning curve ?
Slow 12%, Intermediate 53%, Fast 35%
Do you easily find R/Bioconductor codes, scripts, workflows ?
Yes 35%, No 65%
How do you describe your experience in R/Bioconductor ?
Beginner 18%, Intermediate 53%, Experienced 29%
Do you think an R/Bioconductor community could help to enhance your develoment ?
Yes 82%, No 0%, I don't know 18%
These stats illustrate the importance of having such collaborative platform website allowing bioinformaticians and computational biologists REALLY and EFFECTIVELY collaborate and enhance their developments.
I already developed a prototype (90% of the development is already done), a possible annoucement is possibly planned for the last week of January or early February, although the website is already hosted and effectively running, I will need help to test it and report eventual bugs and problems. The website is intuitive, easy to use and well designed, it recquire a free subscription, users will edit their profile and they are offered a "Submitter tool" to post their source code in three simple steps :
1 - Information about the source code authors (could be the website member or another author cited) 2- Information about the source code itself (dependencies, external libraries, what it do exactly etc ..) 3- Source code Input, output and the code itself.
I will need contributors and beta testers for this website and I will happy to count you among the beta testers of this new developed tool.
Please let me know as soon as possible if you are willing to participate in the website evaluation and testing sending as much source codes as you can.
Kind regards and Happy new year.
PS : Some biojava and bioperl users proposed to extend the website to java and perl, what I in fact did adding also biopython.
If you are interested in sharing your source codes please contact me asap through this website and put as subject : Sharing Source Codes