Personal Thoughts on Collaboration and Long-Term Project Planning: Long-Term Maintenance / Support

I decided to go ahead and post this because of an article by Adam Siepel that I read today, describing broader need to take maintenance / support into consideration for projects (and I previously already had most of this content in a draft).  For example, I thought it was interesting that he brought up the R50 Research Specialist Grant.

In terms of my own personal experience, needing to provide support for COHCAP outside of working hours (back in 2018) was one factor that made it clear to me that the "templates" would have issues with support if I continued to expand topics of research at that previous rate (and that I needed to focus on fewer projects more in-depth).

That said, my individual opinion is that it would be inappropriate to convert COHCAP to have a fee-based license, because having a variety of free programs that can be tested for each project has been very helpful to me (and I recommended testing both COHCAP and methylKit for projects, since I couldn't guarantee any strategy would work out for any particular project).  My impression of DNA.land was also somewhat similar: I think it is good as a free option, but I don't think it would be appropriate to charge for the results that I saw (so, I hope I have misunderstood something about their transition plans).  However, that leaves open the question about what should be done for support (to avoid accumulation of over-time hours as more algorithms are developed).

One thought is that maybe suggest a donation to City of Hope for $10 per project, whenever users find the software helpful would be appropriate (or for some possibly larger amount, from non-scientists that want to keep open-source software free but maintained).  However, I would guess that I have already raised a larger amount through (general) matching funds, so I don't think this is especially urgent.

Otherwise, in terms of alternative funding strategies (instead of patents / licences), these are some ideas that I had:

a) Charge for in-person training of open-source programs / databases?  Allow public (and possibly delayed) free support but charge if providing private support via e-mail?

b) Maybe have small grants for software training / support? Perhaps have a target of a 50-70k salary for a bioinformatician in the lab?  If that is not enough, consider a 100-150k grant for 2 support staff for 1 program (and also encourage users to participate in discussions with other analysts, such as on Biostars, to get a variety of opinions).  This was also briefly discussed in this article on how to support open-source software.  More recently, I think this would also be like the Chan Zuckerberg "Essential Open Source Software for Science" grant.

I hope this doesn't become an issue (like for KEGG, or RepBase, as I understand it), but I noticed that there is a NCBI link to OMIM as well as the OMIM.org link that suggests a donation.  So, perhaps a mix of donations and grant funding covers their needs?

Even in terms of the above options, I tested out the "Developer" support for AWS, but I didn't actually get a response within 24 hours (and ended up solving the problem on my own after that, and reverting back to the free "Basic" plan): so, if you do charge for support, you have to be able to be capable of having prompt, daily discussions to work toward being able to solve user difficulties in a variety of contexts.

As another example, I recently canceled my subscription to the New York Times.  At $4/month, the cost was reasonable.  However, due to the extra effort to view the articles on public computers, I essentially stopped reading the articles.  When I thought about it, I already donate $3/month to Wikipedia.  So, the cost isn't really the limitation: the barriers added by the license / subscription (and the relatively good content that I can get for free) are the reason that I stopped supporting the New York Times.  If they did something similar to Wikipedia (at least for some articles), then I would support them (and, likewise, perhaps I should increase my donation to Wikipedia).

I also have these ideas about limits / suggestions for the use of commercial bioinformatics software, which is kind of like an extension for this post (and this was also discussed in the Genome Biology paper that I read when I first made the post public).

Change Log:
7/30/2019 - public post date
7/31/2019 - trim 1st and 2nd paragraph; add NYT example
8/5/2019 - add matching link and de-emphasize grant
8/6/2019 - minor change
8/12/2019 - add link to RepBase subscription
9/11/2019 - change assumption that donation requires non-profit model
9/16/2019 - add link for DNA.land
11/21/2019 - add link for Chan-Zuckerberg open-source software funding

What About Bioinformatics Companies?

A product starting under a grant (such as in academics or a non-profit) but later being becoming a start-up (as a for-profit) is one possibility. However, my post on providing generics through non-profits would bring into question whether such a start-up could continue to be an independent non-profit (and/or a government entity/contract).

While I think I need to learn more before being able to say something strictly can't be provided from a for-profit organization, I think there are some things that may need to be taken into consideration within the current framework of options:

• Perhaps require free command-line version of software for commercial software with a user interface (and emphasize the education component to learn more coding)?  Otherwise, it isn't really reproducible for most people, and it probably isn't appropriate to only use one program in all situations.
• In terms of compromises to help with reproducibility, Novoalign has free version that uses fewer threads, and MATLAB allows people to run programs developed in MATLAB without a licence .
• precisionFDA is designed/supported by a private company (DNAnexus), though what I assume is a government contract.  So, if you have genomics data, it is free to re-analyze / compare your own genomics data (since the FDA is paying for the costs).  I think this is a very good thing for citizens that can help them become more involved (and, hopefully, understand the difficulties of the regulatory process a little better).  I have some notes on on my own experiences with precisionFDA here.  So, I support this strategy (although perhaps there can be discussion about the fact that DNAnexus is currently a for-profit company).

Also, the idea that encouraging the testing multiple free RNA-Seq methods (something else that I would like to be able to show, at some point) may seem at ends with having commercial bioinformatics software.  While there is some truth to this, I would have the following response to such a critique:

1) I think the time frame matters when discussing software recommendations.  If the goal is to increase coding abilities in 5-10 years, then papers that need to be published sooner may need some alternative solution.  In other words, if somebody doesn't know how to code and there is a program with a graphical user interface that helps them do some analysis on their own, I think that can be good.  However, if they get a weird result (and/or a negative result) with that program (which could have a commercial license), I strongly suggest they test other programs before preparing for publication (and those other programs may need to be open-source command line programs)

2) Having extra options (which includes commercial software) gives labs more options of programs that they can test for their project.  So, if you get a weird result with the open-source software, having extra commercial options may help.  My only concern is that the fees may be a barrier to entry for some labs, and I don't want to encourage excessive use of free trials if licenses are not often eventually purchased.

So, I think there is still value in giving suggestions of how to make the most out of available open-source options, even you use use some commercial programs.  This is similar to what I do: the majority of the bioinformatics programs that I use are open-source, but I sometimes also use commercial programs (like IPA).  However, even with IPA, I would also recommend comparing results with free programs (like Enrichr).  Sometimes the free open-source programs end up being a better fit for the individual project than the commercial ones, but that often varies by project.

However, if you can't lock down one particular program to use in all situations (which has definitely been my experience), that is why I am somewhat concerned about the barriers to entry that could be caused by having to purchase licenses (and, if you don't already have a license, I would usually recommend trying out open-source options first).  I think this is also helps with your ability to provide support during transitions.  For example, I code in R rather than MATLAB, so I don't have to worry about keeping a MATLAB license (and a lot of genomics packages are developed in R/Bioconductor, in addition to it being free).

Change Log:
6/15/2019 - public post date