Note
We would like to thank everyone who sent us a letter of support – altogether with previous submission we have received 64 letters. Thank you very much.
We have (re-)submitted the grant proposal on July 1st before the deadline and hope to hear from the NIH late Fall 2011. If you still want to express your support or just share your positive (or negative) experience, please comment on the Testimonials page.
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)).
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:
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?
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.
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 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, 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, 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
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;
integrate essential Matlab-based open-source software: e.g., BrainStorm, EEGLAB, Fieldtrip, PsychToolbox, SPM;
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;
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
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;
develop new test suites for common heterogeneous analysis pipelines and run them routinely to assure proper functioning and ongoing compatibility of all involved tools;
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
employ Debian’s existing software archive snapshotting framework to preserve and distribute all previous and current versions of supported software in NeuroDebian;
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
provide binary packages for Debian-derived operating systems (e.g., Ubuntu);
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;
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.