1 :date: 2011-06-15 10:00:00
2 :tags: neuroscience, grant
6 We would like to thank everyone who sent us a letter of support --
7 altogether with previous submission we have received 64
8 letters. *Thank you very much*.
10 We have (re-)submitted the grant proposal on July 1st before the
11 deadline and hope to hear from the NIH late Fall 2011. If you
12 still want to express your support or just share your positive (or
13 negative) experience, please comment on the
14 :ref:`testimonials` page.
16 NeuroDebian needs your support
17 ==============================
19 The NeuroDebian Team is asking for your support. We are hoping to obtain
20 funding for continued maintenance, development and expansion of the project.
21 An initial grant proposal has already been reviewed and we are about to
22 resubmit to address reviewer comments (PI `Dr. James V. Haxby`_; NIH program
23 announcement PAR-08-010_: Continued Development and Maintenance of Software
26 .. _Dr. James V. Haxby: http://haxbylab.dartmouth.edu/ppl/jim.html
27 .. _PAR-08-010: http://grants.nih.gov/grants/guide/pa-files/par-08-010.html
29 Please see the abstract and specific aims at the end for a more
30 detailed description of the updated project proposal.
32 We need to address two main reviewer concerns:
34 1. **Proof of the state of the project**
36 We previously failed to convince the reviewers that our efforts
37 **already** help researchers to maintain a productive research
38 software environment with minimal effort. Therefore, if you are
39 using NeuroDebian, and you feel that it is beneficial for your
40 research activities, we would appreciate your letter of support
41 describing: Why did you start using NeuroDebian? What do you use it
44 2. **Feasibility of virtual environments for software deployment**
46 The reviewers argued that using a virtual environment (i.e. a virtual
47 machine, VM) is not a feasible solution to the problem of deploying an
48 integrated platform, like NeuroDebian, on the two major non-GNU/Linux
49 operating systems (Windows and Mac OS). Therefore, we would appreciate your
50 letter of support, if you rely on a VM to run or evaluate research software.
51 Such letter would preferably describe why you use a VM, and could offer a
52 short summary of the VM experience in your research activities.
54 We also appreciate letters on other aspects of the proposal, and would be
55 delighted to see requests for any particular functionality included in them.
57 If you would like to see the NeuroDebian project to continue its development,
58 we would be thankful if you send your "Letter of Support" via email_
59 (preferably a PDF) or fax (+1 (603) 646-1419) to provide additional weight for
60 our application. For your convenience, we have composed a generic `letter
63 .. _email: team@neuro.debian.net
64 .. _letter template: http://neuro.debian.net/_files/letter_of_support_template.txt
66 If you have previously provided us a letter of support, and either
67 want to retract or alter it, based on the updated project description,
70 We would appreciate if we receive your letter of support within a
71 week, so we are still on time with the resubmission and ready to
72 dedicate ourselves to HBM 2011 (visit us at booth #108).
74 Thank you very much in advance for your support,
82 Complex software systems play a more and more important role in neuroscience
83 research and managing an appropriate research environment is becoming
84 increasingly difficult. `NeuroDebian <http://neuro.debian.net>`_ is a turnkey
85 research software platform for all aspects of the neuroscientific research
86 process. It takes the ideas of the Neuroimaging Tools and Resources
87 Clearinghouse (`NITRC <http://www.nitrc.org>`_, on maximizing research
88 transparency and methods sharing, one step further, by providing a
89 comprehensive suite of readily usable and fully integrated software with a
90 robust testing and deployment infrastructure. Consequently, it improves
91 interoperability among the tools and frees researchers from the burden of
92 tedious installation or upgrade procedures. That, in turn, positively affects
93 their availability for actual research activities, as well as their motivation
94 to test new analysis tools and stay connected with the latest methodological
95 developments in the field.
97 Over the past six years, NeuroDebian has integrated dozens of neuroscience
98 software tools into the `Debian operating system <http://www.debian.org>`_,
99 making its current version, Debian 6.0, the first operating system world-wide
100 with comprehensive built-in support for MRI-based neuro-imaging research. In
101 close collaboration with the Debian community and all involved neuroscience
102 research groups we have provided middleware support for users and developers –
103 consulting developers regarding release practices and legal aspects and
104 streamlining technical support of NeuroDebian users. This joint effort has been
105 well received by the research community, and, according to a recent survey,
106 GNU/Linux-based systems are now the most common computing platform in
107 neuroscience, and NeuroDebian is the most popular software resource dedicated
110 To further contribute to the dissemination of new methods, the NeuroDebian
111 project aims to expand its coverage of software and to assure robust operation
112 across a wide variety of deployment scenarios. Developing an environment with a
113 large number of tightly integrated neuroscience software tools will allow for
114 testing efforts that continuously verify software interoperability. We will
115 develop a framework to derive a comprehensive description of a NeuroDebian
116 analysis environment, and offer anyone the building blocks to, later on,
117 reincarnate an identical copy, thus addressing an essential aspect of
118 reproducible research. By means of virtualization solutions we will offer
119 researchers the tools to take advantage of NeuroDebian on non-GNU/Linux
120 operating systems, and advanced computing platforms (e.g., distributed and
121 cloud computing) for efficient large-scale data analysis and modeling.
123 By fostering proven and efficient practices of the free and open-source
124 software community in neuroscience, NeuroDebian will help to assure the
125 availability and continued usefulness of existing software.
131 This project aims to further improve integration of neuroscience
132 software into the larger free and open source software community by
133 adopting standards and practices that have proven to yield a maximum
134 of quality and productivity. To this end, we will keep working closely
135 with a large number of neuroscience software developers, as well as
136 the Debian community. In particular we aim to achieve:
138 Aim 1: Ongoing maintenance of neuroscientific software in (Neuro)Debian
139 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
141 NeuroDebian currently maintains over 30 software projects, from
142 single-purpose tools to complex analysis suites. All integrated
143 software requires timely response to bug reports, and software
144 updates. We aim to continue to offer reliable and prompt service in
145 providing an efficient research environment.
147 Aim 2: Increased coverage of neuroscientific research tools
148 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
150 To enhance the utility of NeuroDebian for a wide range of research
153 a) extend software coverage beyond (f)MRI/DTI-based neuroimaging to
154 tools for intra/extra-cellular recording and modeling, EEG/MEG,
155 and data management: e.g., BrainVisa/Anatomist, Camino, DTI-TK,
156 FreeSurfer, NEURON, XNAT, and other software that becomes
157 available during the project lifetime;
158 b) integrate essential Matlab-based open-source software: e.g.,
159 BrainStorm, EEGLAB, Fieldtrip, PsychToolbox, SPM;
160 c) facilitate work on increasing the compatibility of Matlab-based
161 neuroscience tools with alternative open-source computing
162 platforms – such as Octave – to improve their availability in
163 high-throughput, and cloud computing environments and loosen
164 dependencies on proprietary systems;
165 d) mentor interested developers in maintaining their software in
166 Debian by themselves.
168 Aim 3: Quality and interoperability assurance
169 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
171 Independent research software tools evolve at their own pace. This
172 poses a challenge for heterogeneous computing environments. To
173 assure reliability and interoperability without stagnation we will
175 a) exercise available test batteries on recent and upcoming releases
176 of Debian and Ubuntu to assure robust performance and inform
177 developers about upcoming changes before researchers are affected;
178 b) develop new test suites for common heterogeneous analysis
179 pipelines and run them routinely to assure proper functioning and
180 ongoing compatibility of all involved tools;
181 c) make developed test suites readily available to users so they can
182 verify correct operation of their particular research
185 Aim 4: Sustained availability of software and precise re-creation of complete research environments
186 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
188 The scientific workflow frequently requires re-analyses of data with
189 particular versions of software, for example, to revise a manuscript
190 or to reproduce a study. We will
192 a) employ Debian’s existing software archive snapshotting framework
193 to preserve and distribute all previous and current versions of
194 supported software in NeuroDebian;
195 b) build on Debian’s package management systems, to develop tools to
196 describe a particular analysis environment (with all versioned
197 dependencies) to be able to reconstruct it at any later point in
198 time – by anyone – given access to the specification and to the
199 software archive snapshots.
201 Aim 5: Broad availability of NeuroDebian on common and advanced computing platforms
202 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
204 A NeuroDebian-based system is not bound to computers solely running
207 a) provide binary packages for Debian-derived operating systems
209 b) provide a virtual appliance allowing deployment of NeuroDebian in
210 a virtualized environment on proprietary operating systems
211 (e.g., Microsoft Windows and Mac OS X), as well as on other
212 non-Debian GNU/Linux distributions;
213 c) provide NeuroDebian system images for cloud and high-throughput
214 computing that are compatible with popular service providers and
215 environments, such as Amazon EC2, and Condor.