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The first opportunity to comment on bioinformatics since my non-compete/nda is over! This seems like a very sloppily put together list of myths, but I'll bite

The first opportunity to comment on bioinformatics since my non-compete/nda is over! This seems like a very sloppily put together list of myths, but I'll bite anyway. 1. Not true, but I think that's largely because much of the software used is closed so the FOSS community is largely anemic in the bio world. For the tools that are FOSS or BSD, I saw plenty of contributions, but the other thing to keep in mind is that it's not just about the programming. You have to have a certain level of understanding of the application domain to program a solution for it properly, and there are very few of these people around. I predict a huge uptick in demand and salaries for bioprogrammers. 2. Is true. You need your own people on salary to program for your needs. I was the sysadmin part of a phd, sysadmin, programmer team and we were doing stuff that no-one else was going to do for us. You need to have your own programmer, and a good sysadmin, full stop. 3. Is also true. Picking the right license is important because many labs are pretty tight on cash flow. Sure, they probably have millions going through them a month, but operating costs are super high and margins are lower than you may think. It was during my time in the genetics lab that I fully realized why FOSS was so important, and I think it's the future. (with a few key proprietary exceptions that no FOSS has matched yet, (think Elmer vs Comsol)) 4. Using a FOSS license makes this a moot point to address. Use GPLv3 code people, stop using BSD! 5-9: not worth addressing. Anyway, my overall view of the field is this: with sequencing getting cheaper, the problem is in managing the levels of data being generated (sysadmin issue) and in interpreting the data for meaningful results (programmer/phd issue). Personally, I think that machine learning is going to be the right breakthrough to follow and apply to bio, and once we do that I expect it to take off to crazy levels. I'm talking sequencer in every doctors office, and artificial genetic manipulation becoming much easier and with more accurate predictions. Also, the other thing everyone underestimates is the microbiome as an entity. You are more the bacteria that lives in you than you are you. Of course, I struggle to understand the science sometimes, I'm just a sysadmin, so take what I say with a grain of salt.

dragonwriter 11y ago
You may be confusing "FOSS" (Free/Open Source Software) with copy BSD is F/OSS, it is not copyleft. GPLv3 is both F/OSS and copyleft.
- arca_vorago 11y ago
  Not confused, its just that when I say FOSS I think FSF aligned licenses, eg, FOSS = Free AND Open Source Software != Free/Open Source Software. I feel like its an important distinction. That being said, I understand thats now how most view the phrase so I will adjust verbiage accordingly.
  - dragonwriter 11y ago
    > Not confused, its just that when I say FOSS I think FSF aligned licenses, eg, FOSS = Free AND Open Source Software BSD License is both Free Software per the FSF and Open Source per OSI. In practice, pretty much all FSF-recognized Free Software licenses are OSI-recognized Open Source licenses and vice versa.
    - arca_vorago 11y ago
      I stand corrected, thanks for the info.
roel_v 11y ago
"2. Is true. You need your own people on salary to program for your needs." I think what he was saying is "do it all yourself", the opposite of you interpreted it, it seems. But maybe I got it wrong.
dalke 11y ago
1. "the FOSS community is largely anemic in the bio world" I'm shocked by that. I think of the bio world as having a lot of FOSS software. With BOSC it even has its own yearly (satellite) conference. By comparison, I work in chemical informatics, and think that FOSS availability in chemistry is rather less than biology. I've blamed money - chemists have a longer history of making money from their research than biologists. Which research field do you think has a robust FOSS community and where there are also for-profit companies developing commercial in the same field? 2. "You need to have your own programmer, and a good sysadmin". You say that myth is true, while Pachter thinks it's false. Your disagreement is really more one of team size. Pachter's myth concerns "a large team." You have a team made of a handful of people. That is, Pachter wrote: "I agree with James Taylor, who ... stated that ”... Scientific software is often developed by one or a handful of people.”", which is what you have. I can agree that it's not clear from the text that the myth concerns, having ~6 or more people in the team. 3. Could you explain why your explanation makes the myth true? Pachter gave the example of the UCSC genome browser. From its web site, "The Genome Browser, Blat, and liftOver source are freely downloadable for academic, noncommercial, and personal use. For information on commercial licensing, see the Genome Browser and Blat licensing requirements." Were you working in a for-profit genetics lab when you realized that FOSS was so important? Otherwise, how would a restriction like the UCSC one have affected you? 4. I actually think the FOSS vs. licensing cost are somewhat orthogonal issues. I distribute my software under the MIT license, but only to those people who pay me about US $25,000. This is something the FSF encourages, as a way to bring revenue to a project. However, it only works because I'm not trying to establish some sort of "community" but prefer a vendor/customer relationship. BTW, I think points #1, #2, #3, and #5 can be recast as "you need to build a community around your project." I think that's a myth in its own right.
- infinite8s 11y ago
  "4. I actually think the FOSS vs. licensing cost are somewhat orthogonal issues. I distribute my software under the MIT license, but only to those people who pay me about US $25,000. This is something the FSF encourages, as a way to bring revenue to a project. However, it only works because I'm not trying to establish some sort of "community" but prefer a vendor/customer relationship." Why the MIT license then? Do you figure that people who paid $25k for the software aren't going to go upload it to github for all to see?

dragonwriter 11y ago

You may be confusing "FOSS" (Free/Open Source Software) with copy BSD is F/OSS, it is not copyleft. GPLv3 is both F/OSS and copyleft.

arca_vorago 11y ago
Not confused, its just that when I say FOSS I think FSF aligned licenses, eg, FOSS = Free AND Open Source Software != Free/Open Source Software. I feel like its an important distinction. That being said, I understand thats now how most view the phrase so I will adjust verbiage accordingly.
- dragonwriter 11y ago
  > Not confused, its just that when I say FOSS I think FSF aligned licenses, eg, FOSS = Free AND Open Source Software BSD License is both Free Software per the FSF and Open Source per OSI. In practice, pretty much all FSF-recognized Free Software licenses are OSI-recognized Open Source licenses and vice versa.
  - arca_vorago 11y ago
    I stand corrected, thanks for the info.

roel_v 11y ago

"2. Is true. You need your own people on salary to program for your needs." I think what he was saying is "do it all yourself", the opposite of you interpreted it, it seems. But maybe I got it wrong.

dalke 11y ago

1. "the FOSS community is largely anemic in the bio world" I'm shocked by that. I think of the bio world as having a lot of FOSS software. With BOSC it even has its own yearly (satellite) conference. By comparison, I work in chemical informatics, and think that FOSS availability in chemistry is rather less than biology. I've blamed money - chemists have a longer history of making money from their research than biologists. Which research field do you think has a robust FOSS community and where there are also for-profit companies developing commercial in the same field? 2. "You need to have your own programmer, and a good sysadmin". You say that myth is true, while Pachter thinks it's false. Your disagreement is really more one of team size. Pachter's myth concerns "a large team." You have a team made of a handful of people. That is, Pachter wrote: "I agree with James Taylor, who ... stated that ”... Scientific software is often developed by one or a handful of people.”", which is what you have. I can agree that it's not clear from the text that the myth concerns, having ~6 or more people in the team. 3. Could you explain why your explanation makes the myth true? Pachter gave the example of the UCSC genome browser. From its web site, "The Genome Browser, Blat, and liftOver source are freely downloadable for academic, noncommercial, and personal use. For information on commercial licensing, see the Genome Browser and Blat licensing requirements." Were you working in a for-profit genetics lab when you realized that FOSS was so important? Otherwise, how would a restriction like the UCSC one have affected you? 4. I actually think the FOSS vs. licensing cost are somewhat orthogonal issues. I distribute my software under the MIT license, but only to those people who pay me about US $25,000. This is something the FSF encourages, as a way to bring revenue to a project. However, it only works because I'm not trying to establish some sort of "community" but prefer a vendor/customer relationship. BTW, I think points #1, #2, #3, and #5 can be recast as "you need to build a community around your project." I think that's a myth in its own right.

infinite8s 11y ago
"4. I actually think the FOSS vs. licensing cost are somewhat orthogonal issues. I distribute my software under the MIT license, but only to those people who pay me about US $25,000. This is something the FSF encourages, as a way to bring revenue to a project. However, it only works because I'm not trying to establish some sort of "community" but prefer a vendor/customer relationship." Why the MIT license then? Do you figure that people who paid $25k for the software aren't going to go upload it to github for all to see?