Dear Dr. Gibson,
I hope you are well. Release of the source code for TRF under a Free or Open Source license would be greatly appreciated. Thank you very much for your contributions to science, Cheers, -- Michael R. Crusoe Co-founder & Lead, Common Workflow Language project [email protected] On Tue, Jun 26, 2018, 10:27 Andreas Tille <[email protected]> wrote: > Hi again, > > I have checked the download page of trf[1] but there is no new release. > I wonder what might be the progress of a release under a free license. > May be you switched to some Git development platform and I just missed > the move? > > Kind regards > > Andreas. > > [1] https://tandem.bu.edu/trf/trf.download.html > > On Thu, Oct 12, 2017 at 10:45:28PM +0200, Andreas Tille wrote: > > Hi Yozen, > > > > thanks for the helpful and long term promising answer. > > > > Kind regards > > > > Andreas. > > > > On Thu, Oct 12, 2017 at 04:17:59PM -0400, Yozen Hernandez wrote: > > > Hi Andreas, > > > > > > So far, no change from the last time we spoke. > > > > > > However I can say that the long term goal is to release TRF under an > open > > > source license, and we have been looking to do this for a while. We > have > > > some things we'd like to get done with the code first and then we will > pick > > > an open source license and release the code. However, we don't have a > set > > > timeline on this at the moment. > > > > > > If I am still in this lab at that time I will be sure to update you > all on > > > the status. For future questions about TRF being released please > contact > > > our lab's PI Dr. Gary Benson at [email protected]. I can be contacted > about > > > development questions, bugs, etc, but I may take some time to respond > and > > > address most issues. > > > > > > Thanks & best, > > > Yozen > > > > > > *Yözen Hernández* > > > *Graduate Program in Bioinformatics, PhD Candidate* > > > *Laboratory for Biocomputing and Informatics* > > > *Boston University* > > > *(347) 829-6936 - [ (347) 82YOZEN ]* > > > > > > On Fri, Oct 6, 2017 at 4:36 PM, Andreas Tille <[email protected]> > wrote: > > > > > > > Hi Yozen, > > > > > > > > more than one year ago and one Debian release later I'd like to > refresh > > > > my question: Do you have any news about freeing Tandem Repeat > Finder? > > > > > > > > Kind regards > > > > > > > > Andreas. > > > > > > > > On Wed, Jun 22, 2016 at 11:02:28AM +0200, Andreas Tille wrote: > > > > > Hi Yozen, > > > > > > > > > > thanks for your hint and understanding - I'll write to Gary Benson. > > > > > > > > > > Kind regards > > > > > > > > > > Andreas. > > > > > > > > > > On Sun, Jun 19, 2016 at 12:12:55PM -0400, Yozen Hernandez wrote: > > > > > > Dear Michael and the rest of the Debian Medical Team, > > > > > > > > > > > > Sorry again for the long response time. I should clarify that I > am > > > > only the > > > > > > current maintainer of TRF, and have no say over whether or not it > > > > becomes > > > > > > open source. For further inquiries regarding TRF, please contact > the > > > > > > original author, and my PI, Dr Gary Benson at [email protected]. > > > > > > > > > > > > As for all of your arguments regarding the importance of open > source > > > > > > software, especially in science, please know that I completely > agree > > > > with > > > > > > you on every point. I am personally a strong supporter of open > source > > > > > > software, and everything that I write myself I either have > released, or > > > > > > plan to release under an open source license. > > > > > > > > > > > > Thanks for all your interest. > > > > > > > > > > > > Best, > > > > > > Yozen > > > > > > > > > > > > > > > > > > *Yözen Hernández* > > > > > > *Graduate Program in Bioinformatics, PhD Candidate* > > > > > > *Laboratory for Biocomputing and Informatics* > > > > > > *Boston University* > > > > > > *(347) 829-6936 - [ (347) 82YOZEN ]* > > > > > > > > > > > > On Fri, May 27, 2016 at 4:31 AM, Michael Crusoe < > > > > [email protected]> > > > > > > wrote: > > > > > > > > > > > > > Dear Yozen, > > > > > > > > > > > > > > As a research software engineer who works with sequencing > analysis > > > > > > > researchers I join Andreas in asking you to release Tandem > Repeat > > > > > > > Finder under a free license. > > > > > > > > > > > > > > I see that you have been funded with NSF grants, that is great! > > > > > > > However, to treat the public ethically, the software should be > > > > free—as > > > > > > > in freedom—for the whole public. This means the freedom to > read the > > > > > > > source code so that they may understand it better, the freedom > to > > > > > > > modify the source code so that they may improve upon it, and > the > > > > > > > freedom to redistribute the source code and their > modifications so > > > > > > > that they may share bug fixes and new features. > > > > > > > > > > > > > > Many researchers actively avoid non-open-source software, see a > > > > > > > discussion from my previous boss C. Titus Brown: > > > > > > > > http://ivory.idyll.org/blog/2015-on-licensing-in-bioinformatics.html > > > > > > > under "Why avoid non-open-source software?" > > > > > > > > > > > > > > One of the many benefits I have enjoyed with releasing my > software > > > > > > > under a free or open source license is the improvements I get > from > > > > > > > other users. > > > > > > > > > > > > > > TRF is widely used, as I'm sure you know. Unlike most software > that > > > > > > > has been written it has shown to be useful. Sharing the source > code > > > > > > > provides a path to sustainability should you decide to > dedicate your > > > > > > > time to other projects or if you are not able to continue > maintaining > > > > > > > the codebase. > > > > > > > > > > > > > > I hope you take my letter into consideration. If you have any > > > > > > > questions about licensing I would be happy to answer them. > > > > > > > > > > > > > > This is not an obligation to run a community based open source > > > > > > > project, we're just asking for the right to further > redistribute your > > > > > > > work (with prominent attribution!) so that more people can use > it. > > > > > > > > > > > > > > Cheers, > > > > > > > > > > > > > > On Sun, May 15, 2016 at 9:46 AM, Andreas Tille < > [email protected]> > > > > wrote: > > > > > > > > Hi Yozen, > > > > > > > > > > > > > > > > On Thu, May 12, 2016 at 08:11:53PM -0400, Yozen Hernandez > wrote: > > > > > > > >> Dear Andreas, > > > > > > > >> > > > > > > > >> Thank you for contacting about packaging TRF. I indeed > missed your > > > > > > > email. > > > > > > > >> > > > > > > > >> Unfortunately, the source code for TRF is not freely > available. I > > > > do not > > > > > > > >> know the Debian Free Software Guidelines well enough to > decide > > > > whether > > > > > > > or > > > > > > > >> not this is allowed, > > > > > > > > > > > > > > > > The Debian Free Software Guidelines[1] are widely accepted > as Open > > > > > > > > Source definition and it is actually that the source code is > freely > > > > > > > > available. > > > > > > > > > > > > > > > >> but I may have a solution that I have seen other > > > > > > > >> packages use. For instance, the Oracle Java packages I have > seen > > > > ask the > > > > > > > >> user to accept a license agreement. The package script then > goes > > > > on to > > > > > > > >> download the appropriate binary upon acceptance. This could > be > > > > part of > > > > > > > the > > > > > > > >> RepeatMasker package since TRF is required by that > software, and > > > > I can > > > > > > > >> assist by providing the URLs for the i386 and x64 builds. > > > > > > > > > > > > > > > > There are several glitches in this suggestion: > > > > > > > > > > > > > > > > 1. The Oracle Java packages are not part of Debian. > Debian > > > > ships > > > > > > > > with OpenJDK. In so far the comparison is weak. > > > > > > > > 2. For official Debian packages there is no point to ask > for a > > > > > > > > license since the user can be sure that the installed > > > > software > > > > > > > > is per definition free. > > > > > > > > 3. Debian packages can only depend from other Debian > packages > > > > > > > > but not from unofficial ones like Oracle Java or your > > > > suggested > > > > > > > > TRF > > > > > > > > 4. Debian ships for several architectures not only i386 > and x64 > > > > (in > > > > > > > > Debian nomenclature amd64). For instance > architectures like > > > > arm64 > > > > > > > > and ppc64 might become quite interesting in the near > future > > > > and > > > > > > > > we try to care for building on these architectures as > well > > > > > > > > > > > > > > > > So far for the general considerations. In the specific case > of > > > > > > > > scientific software we also consider the free availability > of the > > > > source > > > > > > > > code as very important to prove the correctness of the > results and > > > > > > > > enable reproducibility. So in this case there are extra good > > > > reasons > > > > > > > > for publishing the code. > > > > > > > > > > > > > > > >> Another work around could be to ask the user to manually > download > > > > and > > > > > > > >> install TRF themselves by providing them with the URL to our > > > > downloads > > > > > > > page. > > > > > > > > > > > > > > > > As said above a Debian package is not allowed to depend from > > > > external > > > > > > > > resources. > > > > > > > > > > > > > > > >> I understand that these are not ideal solutions, but for the > > > > forseeable > > > > > > > >> future we will not license TRF under a free software > license. > > > > > > > > > > > > > > > > I have no idea whether this might be open for discussion at > your > > > > site > > > > > > > > and what might be the motivation to keep the code of a > scientific > > > > tool > > > > > > > > closed. In case you might like to re-think it I'd like to > point > > > > out > > > > > > > > the following advantages: > > > > > > > > > > > > > > > > Due to the work of the Debian Med team Debian and its > derivatives > > > > like > > > > > > > > Ubuntu gained quite some coverage in biological research. > > > > Providing TRF > > > > > > > > via Debian packages does not only simplify the installation > and > > > > > > > > maintenance for users (you might keep cluster installations > in > > > > mind). > > > > > > > > > > > > > > > > The fact that we are providing so called metapackages > depending > > > > from all > > > > > > > > biological applications installing any application you see > on this > > > > so > > > > > > > > called tasks page[2] might bring TRF automatically on users > > > > computers > > > > > > > > who might become aware of your tool just because it is > included > > > > here and > > > > > > > > you might gain additional users of your software. > > > > > > > > > > > > > > > > As you can see on the tasks page[2] we also put some > importance on > > > > > > > > specifying the according publications which gives the > authors of > > > > the > > > > > > > > software some extra credit. > > > > > > > > > > > > > > > > I could give several more good reasons but I don't know your > > > > motivation > > > > > > > > to keep the source code closed and may be you could rethink > the > > > > decision > > > > > > > > by including the arguments above. > > > > > > > > > > > > > > > > Kind regards > > > > > > > > > > > > > > > > Andreas. > > > > > > > > > > > > > > > > [1] https://www.debian.org/social_contract#guidelines > > > > > > > > [2] http://blends.debian.org/med/tasks/bio > > > > > > > > > > > > > > > > -- > > > > > > > > http://fam-tille.de > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >
