--- /dev/null
+:date: 2011-06-15 10:00:00
+:tags: neuroscience, grant
+
+NeuroDebian needs your support
+==============================
+
+The NeuroDebian Team is asking for your support. We are hoping to obtain
+funding for continued maintenance, development and expansion of the project.
+An initial grant proposal has already been reviewed and we are about to
+resubmit to address reviewer comments (PI `Dr. James V. Haxby`_; NIH program
+announcement PAR-08-010_: Continued Development and Maintenance of Software
+(R01)).
+
+.. _Dr. James V. Haxby: http://haxbylab.dartmouth.edu/ppl/jim.html
+.. _PAR-08-010: http://grants.nih.gov/grants/guide/pa-files/par-08-010.html
+
+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_
+(preferably a PDF) or fax (+1 (603) 646-1419) to provide additional weight for
+our application. For your convenience, we have composed a generic `letter
+template`_.
+
+.. _email: team@neuro.debian.net
+.. _letter template: http://neuro.debian.net/_files/letter_of_support_template.txt
+
+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 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
+
+
+Proposal 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 compatibility 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 to reproduce 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.
projects / neurodebian.git / commitdiff