From: Michael Hanke Date: Wed, 15 Jun 2011 13:01:13 +0000 (-0400) Subject: Funding blog. X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=157970f806eeb405c9914a421b1c78fa14e7c5e4;p=neurodebian.git Funding blog. --- diff --git a/sphinx/_static/neurodebian.css b/sphinx/_static/neurodebian.css index 2ec9140..19fd8cf 100644 --- a/sphinx/_static/neurodebian.css +++ b/sphinx/_static/neurodebian.css @@ -684,6 +684,10 @@ img.logo { border: 0; } +ol.loweralpha { + list-style: lower-alpha; +} + /* Epigraphs */ diff --git a/sphinx/blog/2011/2011-06-15_letter_of_support.rst b/sphinx/blog/2011/2011-06-15_letter_of_support.rst new file mode 100644 index 0000000..8ec1dd5 --- /dev/null +++ b/sphinx/blog/2011/2011-06-15_letter_of_support.rst @@ -0,0 +1,203 @@ +: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 `_ 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 + +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. diff --git a/sphinx/blog/2011/index.rst b/sphinx/blog/2011/index.rst new file mode 100644 index 0000000..401c15f --- /dev/null +++ b/sphinx/blog/2011/index.rst @@ -0,0 +1,9 @@ +2011 +==== + +.. toctree:: + :maxdepth: 1 + :glob: + + 2011* + diff --git a/sphinx/blog/2011/pics b/sphinx/blog/2011/pics new file mode 120000 index 0000000..1bbd53b --- /dev/null +++ b/sphinx/blog/2011/pics @@ -0,0 +1 @@ +../../pics \ No newline at end of file diff --git a/sphinx/blog/index.rst b/sphinx/blog/index.rst index faabef3..c3d78fa 100644 --- a/sphinx/blog/index.rst +++ b/sphinx/blog/index.rst @@ -7,3 +7,4 @@ :glob: 2010/index + 2011/index