Hello, The projects of Debian for the Google Summer of Code http://www.google-melange.com/gsoc/homepage/google/gsoc2015 have their focus on the Debian infrastructure. It was quite some earning experience for me, but eventually I have grasped that this was a good thing. However, my personal ambition for Debian comes for a good part from the practical side of it all - it is my Bioinformatics desktop and/or server - and I want that helped by a GSoC, too.
Now Debian is good (best?) with sharing libraries between otherwise independent software packages, but we are yet doing little to help with the inter-operability of those packages. And beyond our Wiki there is nothing that informs others about how to address our daily routine. This GSoC could help Debian (as a whole, not just "Med") to strengthen its ties with upstream and foster developments to help with the interaction of tools and the promotion of such workflows. While I see naturally quite some opportunities in Bioinformatics, I am highly interested to see our other blends address such workflows, too. So this could be a Debian Blend Project. Here some ideas: * Get Gentle (molecular cloning) dissected into several interoperating small command line tools and combine it with a workflow environment The reason for that is that molecular cloning is an iterative process and Gentle (like all other tools for molecular cloning I looked at, correct me if I am wrong) are dysfunctional with a representation of the steps taken to yield a particular amplicon. The workflow is the recipe to pass to the technical assistant. The workflow engine could be Taverna as a start, which is offered as a Debian package by upstream and ... well ... some day my package for it will work, there may be others. * Functional Tutorials We started to look at Youtube to learn about how to use any particular software. This hurts. Just a bit. I would very much like to see something in the lines of how Docker or VIM introduces itself as a template for biological sequence analysis. * Unit Tests Andreas has already been much at it. There should be more. And more. This GSoC could help. I reckon that we could also come up with new ideas about what such tests could work like, for instance when there is no perfect answer to a problem, as in the assembly of complete genomes from short sequences. * FPGA for application acceleration It was amazing to see how quickly the BitCoin folks jumped from GPUs to FPGA to ASICs. There is quite a number of affordable FPGA boards now available that would be good to have closer to our distribution to prepare for application acceleration. This fancy Open Source Laptop https://www.crowdsupply.com/kosagi/novena-open-laptop even has an FPGA within - albeit quite a small one. I would very much like to see something happening to help sharing Open Source hardware descriptions between such devices. ... There is more. Much more. But how is your feeling about it all? Is it a good idea to have this organised in parallel to what the core of Debian is doing? Are such worthwhile projects in the first place? Are there other GSoC organisations that are likely to care for them? Best, Steffen -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/trinity-8d5f6cdf-2c4c-4d23-b2e7-77f47f863665-1412694786441@3capp-gmx-bs33