Good evening,
I am keen to improve the level of standardisation in bioinformatics, as it feels that this is one of the most fundamental barriers to progress that we face / have faced. Other 'industries' or work sectors faced similar barriers in the past when it became apparent that everyone was doing their own thing and had their own idea of how something should be performed. The first example that comes to mind was the formation of the IEEE who eventually set standards that have resulted in the huge rise in global communication systems. In medicine, there are medical boards and regulatory bodies that oversee treatment of patients, and there exist strict ethical codes that must be followed.
...in bioinformatics, what have we got?
Tomorrow, a new program may appear from some part of the world that seems to convincingly process RNA-seq and ChIP-seq data together in order to find statistically significant ncRNA transcripts that regulate the binding of my transcription factor of interest. The developers may put a strong case for everyone to use their program. A month after its release, what happens? - 20 bugs are already identified and the developers have to release a new version, which is itself erroneous.
- What if there was a body that rigorously screened these programs prior to their release (a requirement for publication)?
- What if there was a 'best practices' guide for all types of bioinformatics analyses? - pipelines rigorously tested and proven to function.
I've only been here on Biostars for 2 months but I've been analysing all types of data for many years and one of the main battles that I face on a daily basis arises from the lack of interoperability of data-types and navigating through bugs in programs. Additionally, each time I look, there seems to be a new publication about some program that may never even be used.
I've been fairly impressed by the experience and skills of people here and I believe that we represent the best chance in the World at forming such a international body. I believe that things like Biostars Handbook can help but we have to go further than that and represent ourselves at international conferences that can attract people from various sectors who will actually listen to us. People have a genuine interest in bioinformatics but I feel that we let ourselves down through some of the issues that I've already outlined in this message.
I'll listen to whatever people have to say in response to this and then gauge my next action. I would eventually hope to set-up a conference in Europe, initially, which would represent the first annual meeting of Biostars where we decide what is needed going forward. Luckily I have close colleagues whose sole business is in setting up conferences and bringing people together. I notice that the entire Globe is fairly well represented here, and I personally have close contacts that spread across North and South America, and all across Europe.
Kevin
Yes, this website does a lot to help others understand what's commonly used for something, what's outdated, etc. Prior to joining, I always just went to Google for solutions and invariably found a recommended solution (untested or tested) on Biostars, StackExchange, or something else.
The part on innovation that you mention is interesting. There is a lot of competition out there right now, with seemingly every PhD student wanting to develop their own program and get it into Bioconductor, but then what appears to happen is that they move on and don't take responsibility for maintenance.
There is no good solution for code that goes stale. Unless your current employer uses and/or allows you to maintain code that you own (BBMap suite is one example) there is no financial incentive for a person do so (availability of spare resources and time may be primary factors as well).