[Neurodebian-users] Supporting NeuroDebian to support YOUR computing environment

[Jodene Fine]

Dear Yaroslov,
I am a new and very enthusiastic user. I would be happy to write a
letter of support. Should it go directly to you or to somewhere else?
Email or paper?
Jodene
___________________________________________________
Jodene Goldenring Fine, Ph.D., Assistant Professor
Department of Counseling, Educational Psychology, and Special Education
Michigan State University
440 Erickson Hall
East Lansing MI 48824
517 884-0443  www.educ.msu.edu/cepse/fine

Associate Director
Center for Neurodevelopmental Study
321 A West Fee Hall
East Lansing MI 48824
517 884-0319 www.psychology.msu.edu/CNS

"Be a nice person and see if it works." Fortune Cookie, China Station,
Berkeley, CA circa 1976


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On Tue, Jun 14, 2011 at 12:02 PM, Yaroslav Halchenko
<debian at onerussian.com> wrote:
> Dear NeuroDebian Developers and Users,
>
> The NeuroDebian [1] Team is once again asking for your support.  We
> are hoping to obtain funding for continued maintenance, development
> and expansion of the project.  Our initial grant proposal
> was reviewed and we are about to resubmit it to address reviewer
> comments (PI Dr. James V. Haxby; NIH program announcement PAR-08-010:
> Continued Development and Maintenance of Software (R01)).
>
> Please see the abstract and specific aims at the end for a more
> detailed description of the updated project proposal.
>
> We need to address two main reviewer concerns:
>
> 1. Proof of the state of the project
>
>   We previously failed to convince the reviewers that our efforts
>   _already_ help researchers to maintain a productive research
>   software environment with minimal effort.  Therefore, if you are
>   using NeuroDebian, and you feel that it is beneficial for your
>   research activities, we would appreciate your letter of support
>   describing: Why did you start using NeuroDebian? What do you use it
>   for?
>
> 2. Feasibility of virtual environments for software deployment
>
>   The reviewers argued that using a virtual environment (i.e. a virtual
>   machine, VM) is not a feasible solution to the problem of deploying an
>   integrated platform, like NeuroDebian, on the two major non-GNU/Linux
>   operating systems (Windows and Mac OS). Therefore, we would appreciate your
>   letter of support, if you rely on a VM to run or evaluate research software.
>   Such letter would preferably describe why you use a VM, and could offer a
>   short summary of the VM experience in your research activities.
>
> We also appreciate letters on other aspects of the proposal, and would be
> delighted to see requests for any particular functionality included in them.
>
> If you would like to see the NeuroDebian project to continue its
> development, we would be thankful if you send your "Letter of Support" via
> email [4] (preferably a PDF) or fax [5] to provide additional weight for our
> application.  For your convenience, we have composed a generic letter
> template [6].
>
> If you have previously provided us a letter of support, and either
> want to retract or alter it, based on the updated project description,
> please email [4] us.
>
> We would appreciate if we receive your letter of support within a
> week, so we are still on time with the resubmission and ready to
> dedicate ourselves to HBM 2011 (visit us at booth #108).
>
> Thank you very much in advance for your support,
>
> the NeuroDebian team
>
>
>
> About NeuroDebian project
> -------------------------
>
> If you are using a Debian or Ubuntu operating system for your neuroscience
> research you might already benefit from our efforts of integrating
> neuroscientific software into these platforms.  For the past 6 years our team
> has provided Debian/Ubuntu packaging, maintenance and troubleshooting for open
> source software, such as AFNI, ANTs, BiosSig4C++, Brian, FSL, Caret, Lipsia,
> MRIcron, NiPy(PE), PsychoPy, PyMVPA, PyNN, and Voxbo (see [2] and [3] for more
> complete references).  Having research software developed by different groups
> with different technologies properly integrated into a uniform environment
> allows scientists to easily maintain a versatile up-to-date research
> environment with just of few commands/mouse-clicks and focus on actual research
> instead of tedious system administration tasks.
>
>
> [1] http://neuro.debian.net
> [2] http://neuro.debian.net/pkgs.html
> [3] http://qa.debian.org/developer.php?login=team@neuro.debian.net
> [4] mailto: NeuroDebian Team <team at neuro.debian.net>
> [5] Fax: +1 (603) 646-1419
> [6] http://neuro.debian.net/_files/letter_of_support_template.txt
>
> -----------------------------------------------------------------
>
> Abstract
> ========
>
> Complex software systems play a more and more important role in
> neuroscience research and managing an appropriate research environment
> is becoming increasingly difficult. NeuroDebian
> (http://neuro.debian.net) is a turnkey research software platform for
> all aspects of the neuroscientific research process. It takes the
> ideas of the Neuroimaging Tools and Resources Clearinghouse (NITRC,
> http://www.nitrc.org), on maximizing research transparency and methods
> sharing, one step further, by providing a comprehensive suite of
> readily usable and fully integrated software with a robust testing and
> deployment infrastructure. Consequently, it improves interoperability
> among the tools and frees researchers from the burden of tedious
> installation or upgrade procedures. That, in turn, positively affects
> their availability for actual research activities, as well as their
> motivation to test new analysis tools and stay connected with the
> latest methodological developments in the field.
>
> Over the past six years, NeuroDebian has integrated dozens of
> neuroscience software tools into the Debian operating system
> (http://www.debian.org), making its current version, Debian 6.0, the
> first operating system world-wide with comprehensive built-in support
> for MRI-based neuro-imaging research. In close collaboration with the
> Debian community and all involved neuroscience research groups we have
> provided middleware support for users and developers – consulting
> developers regarding release practices and legal aspects and
> streamlining technical support of NeuroDebian users. This joint effort
> has been well received by the research community, and, according to a
> recent survey, GNU/Linux-based systems are now the most common
> computing platform in neuroscience, and NeuroDebian is the most
> popular software resource dedicated to neuroscience.
>
> To further contribute to the dissemination of new methods, the
> NeuroDebian project aims to expand its coverage of software and to
> assure robust operation across a wide variety of deployment
> scenarios. Developing an environment with a large number of tightly
> integrated neuroscience software tools will allow for testing efforts
> that continuously verify software interoperability. We will develop a
> framework to derive a comprehensive description of a NeuroDebian
> analysis environment, and offer anyone the building blocks to, later
> on, reincarnate an identical copy, thus addressing an essential aspect
> of reproducible research. By means of virtualization solutions we will
> offer researchers the tools to take advantage of NeuroDebian on
> non-GNU/Linux operating systems, and advanced computing platforms
> (e.g., distributed and cloud computing) for efficient large-scale data
> analysis and modeling.
>
> By fostering proven and efficient practices of the free and
> open-source software community in neuroscience, NeuroDebian will help
> to assure the availability and continued usefulness of existing
> software.
>
>
> Specific aims
> =============
>
> This project aims to further improve integration of neuroscience
> software into the larger free and open source software community by
> adopting standards and practices that have proven to yield a maximum
> of quality and productivity. To this end, we will keep working closely
> with a large number of neuroscience software developers, as well as
> the Debian community. In particular we aim to achieve:
>
> Aim 1 Ongoing maintenance of neuroscientific software in (Neuro)Debian
>
>  NeuroDebian currently maintains over 30 software projects, from
>  single-purpose tools to complex analysis suites. All integrated
>  software requires timely response to bug reports, and software
>  updates. We aim to continue to offer reliable and prompt service in
>  providing an efficient research environment.
>
> Aim 2 Increased coverage of neuroscientific research tools
>
>  To enhance the utility of NeuroDebian for a wide range of research
>  applications we will
>
>  a extend software coverage beyond (f)MRI/DTI-based neuroimaging to
>    tools for intra/extra-cellular recording and modeling, EEG/MEG,
>    and data management: e.g., BrainVisa/Anatomist, Camino, DTI-TK,
>    FreeSurfer, NEURON, XNAT, and other software that becomes
>    available during the project lifetime;
>  b integrate essential Matlab-based open-source software: e.g.,
>    BrainStorm, EEGLAB, Fieldtrip, PsychToolbox, SPM;
>  c facilitate work on increasing the compatibili of Matlab-based
>    neuroscience tools with alternative open-source computing
>    platforms – such as Octave – to improve their availability in
>    high-throughput, and cloud computing environments and loosen
>    dependencies on proprietary systems;
>  d mentor interested developers in maintaining their software in
>    Debian by themselves.
>
> Aim 3 Quality and interoperability assurance
>
>  Independent research software tools evolve at their own pace. This
>  poses a challenge for heterogeneous computing environments. To
>  assure reliability and interoperability without stagnation we will
>
>  a exercise available test batteries on recent and upcoming releases
>    of Debian and Ubuntu to assure robust performance and inform
>    developers about upcoming changes before researchers are affected;
>  b develop new test suites for common heterogeneous analysis
>    pipelines and run them routinely to assure proper functioning and
>    ongoing compatibility of all involved tools;
>  c make developed test suites readily available to users so they can
>    verify correct operation of their particular research
>    environments.
>
> Aim 4 Sustained availability of software and precise re-creation of
>  complete research environments
>
>  The scientific workflow frequently requires re-analyses of data with
>  particular versions of software, for example, to revise a manuscript
>  or a reproduction of a study. We will
>
>  a employ Debian’s existing software archive snapshotting framework
>    to preserve and distribute all previous and current versions of
>    supported software in NeuroDebian;
>  b build on Debian’s package management systems, to develop tools to
>    describe a particular analysis environment (with all versioned
>    dependencies) to be able to reconstruct it at any later point in
>    time – by anyone – given access to the specification and to the
>    software archive snapshots.
>
> Aim 5 Broad availability of NeuroDebian on common and advanced
>    computing platforms
>
>  A NeuroDebian-based system is not bound to computers solely running
>  Debian. We will
>
>  a provide binary packages for Debian-derived operating systems
>    (e.g., Ubuntu);
>  b provide a virtual appliance allowing deployment of NeuroDebian in
>    a virtualized environment on proprietary operating systems
>    (e.g., Microsoft Windows and Mac OS X), as well as on other
>    non-Debian GNU/Linux distributions;
>  c provide NeuroDebian system images for cloud and high-throughput
>    computing that are compatible with popular service providers and
>    environments, such as Amazon EC2, and Condor.
>
>
>
>
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