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 > > > > > > > > > > > > > > > > > > > > > -- > > > > Michael R. Crusoe > > > > Community Engineer & Co-founder > > > > Common Workflow Language project > > > > https://impactstory.org/u/0000-0002-2961-9670 > > > > [email protected] > > > > +32 (0) 2 808 25 58 > > > > +1 480 627 9108 > > > > > > > > -- > > http://fam-tille.de > > > > > > -- > http://fam-tille.de >
