Review of Open Science Summit 2010, #OSS2010

I have been attending Open Science Summit 2010 at Berkeley, CA and although not quite finished yet I feel like I can give an overall review of what I thought of the conference. You can check out my individual comments during the conference on Twitter.

I would like to state that in general I am grateful and respect the work that Joseph Jackson and the organizing committee conducted to make this open science conference a reality. It is a tremendous amount of effort and the following is only meant as a constructive criticism for possible open science summit conferences in the future.

Pros

• Bringing together a very intelligent diverse group of speakers. Good mix of policy makers, developers, traditional scientists, biotech, young and old, etc.
  
• Great use of technology. Providing a live video stream of conferences is an idea that I wish more conferences implemented. Also, using backchan.nl is a nice additional add-on that couples well with the live video stream.
• Willingness to try to adapt (as much as possible) to conference attendees comments via twitter, back channel, etc.

Cons

• No scheduled breaks. Breaks are needed for numerous practical reasons: people need bathroom breaks, time to get some fresh air, and time for talks to get back on schedule. Even more importantly, it allows people to mingle. People travel to conferences so that they can get a chance to connect with people face to face (otherwise they would just watch the online feed).
  
• No time for Q & A. Questions immediately after speakers not only is informative, but gives a temporary "mind break" for the audience. It also gives time for IT to get the next presentation queued. Note: this did tend to improve as the conference proceeded.
  
• Too many speakers. Having 25 speakers in a single day (without parallel sessions) is just too much information for people to take in and sit through.

Additional lessons learned

• A no slide presentation is not a guarantee that it will be a good one.
• Videos do not always make a presentation better.
• Having 2 or more speakers from the same organization or having the exact same opinion is not really beneficial.

Comments from FriendFeed

Bioinformatics for biologists

I just read the review "Bioinformatics Software for Biologists in the Genomics Era" by Kumar and Dudley. Basically, the authors outline the need for improved bioinformatics software that can be easily used by biologists. I completely agree with the authors, but by the time I was done reading the article I was somewhat annoyed. I think the overall problem I have is that they just keep reiterating that the people developing the tools need to make them more user friendly, without giving any real review of possible solutions or roadblocks that need to be overcome.
They state that:

1. command-line programs are bad, GUI's are good
   
2. being able to submit batch processes is good
3. documentation is good
4. clear, human readable results is good
5. tools that run on all operating systems is good
   
6. being able to connect multiple tools in a pipeline (with no programming required) is good
   

I think even the most amateur programmer is aware of these issues, so I am left wondering who the audience of the article is meant for? In addition they don't reference any of the current tools that are being developed to improve on the situation. In particular they propose:

"Within the context of the user-friendly software, we favor a solution where the existing implementations of computational methods can be incorporated “as is,” without requiring any significant effort from the developer of the program that is being incorporated. We refer to this approach as “Application Linking,” which is similar to “wrapping” (Spitznagel and Garlan, 2003). The aim of Application Linking is to allow existing user-friendly applications to seamlessly host third-party scripts and applications through its graphical interface, such that the user is abstracted from the intricate nuances of the hosted application’s non-visual execution requirements (e.g., process control, system I/O, and control files)."

Ummm.... I guess they haven't heard of Taverna and web services?

As a student who is writing one of these programs let me elaborate on what I think is the main problem. Scientific credit is based on publishing not on producing good tools. What does this mean to me as a PhD student? It means that the time spent on producing a robust web tool would be better spent on making additional tools or conducting more biological relevant based analyzes that will lead to more publishable papers. Am I proud of this? No. Especially since I have a strong interest in reducing programming redundancy, but for now it seems that I don't have much of a choice.