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
mrc@commonwl.orgHi 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 gbenson@bu.edu. 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 <andreas@an3as.eu> 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 gbenson@bu.edu.
> > > > >
> > > > > 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 <
> > > michael.crusoe@gmail.com>
> > > > > 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 <tille@debian.org>
> > > 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
> > > > > > >
> > > > > >
> > > > > >
> > > > > >
> > >