From: Michael Hanke <michael.hanke@gmail.com>
Date: Thu, 12 May 2011 20:50:08 +0000 (-0400)
Subject: Merge branch 'master' of alioth:/git/pkg-exppsy/neurodebian
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=035c51fd41592ba61e9888d461778c166c826ffd;p=neurodebian.git

Merge branch 'master' of alioth:/git/pkg-exppsy/neurodebian

* 'master' of alioth:/git/pkg-exppsy/neurodebian:
  pollutted survey with list of software
---

035c51fd41592ba61e9888d461778c166c826ffd
diff --cc sandbox/survey.rst
index 6a00f6f,d127e17..896b72a
--- a/sandbox/survey.rst
+++ b/sandbox/survey.rst
@@@ -457,213 -94,186 +457,343 @@@ environment myself
  Virtualization
  --------------
  
 -Do you use it? ``yes, no``
 +The following questions are about your usage of systems for hardware
 +virtualization in your research -- so-called **virtual machines**.
 +Virtualization is a technology that allows running more than one operating
 +systems on one machine at the same time.
  
 -IF
 -~~
 +.. raw:: html
  
 -What solution: ``multi select vbox, vmware, kvm, xem, qemu``
 -On what host system: ``detailed list``
 -With what guest system ``detailed list``
 +   <table>
 +   <tr class="oddrow">
 +   <td class="task">
  
 -Why do you use it: ``multi select``
 +How often do you use virtual machines for your research purposes?
  
 -  - Otherwise software incompatible with my system
 -  - Flexible snapshots
 -  - Portable (test developed software across platforms)
 +.. raw:: html
  
 -What fraction of computing task do you do in a VM?
 +   </td><td class="response">
 +   <select name="pref_time" size="1">
 +   <option value="none" selected="selected" label="Select an option"></option>
 +   <option value="never" label="Never"></option>
 +   <option value="occasionally" label="Occasionally"></option>
 +   <option value="often" label="Often"></option>
 +   <option value="always" label="Exclusively"></option>
 +   </select><div style="font-size:60%">(skip the remaining questions of this section if "never")</div>
 +   </td></tr><tr><td class="task">
  
 -Do you do computing on clusters?
 -Do you do computing in a cloud?
 +Which products for virtualization are you using?
  
 +.. raw:: html
  
 -Software usage
 ---------------
 +   </td><td class="response">
 +   <table><tr><td>
 +   <input type="checkbox" name="" value="" />VMWare<br />
 +   <input type="checkbox" name="" value="" />VirtualBox<br />
 +   <input type="checkbox" name="" value="" />Parallels<br />
 +   <input type="checkbox" name="" value="" />QEMU<br />
 +   </td><td>
 +   <input type="checkbox" name="" value="" />Virtual PC<br />
 +   <input type="checkbox" name="" value="" />Xen<br />
 +   <input type="checkbox" name="" value="" />KVM<br />
 +   <input type="checkbox" name="" value="other" />
 +   <input name="other_vm" type="text" size="20" maxlength="40">
 +   </td></tr></table>
 +   </td></tr><tr class="oddrow"><td>
 +
 +What **guest operating system** is running inside virtual machine?
  
 -What software are you using in your research?
 +.. raw:: html
  
 -? Do you use real-time Linux kernel? if yes, which: ``multi select RTAI, Xenomai, RT_Linux``
 +   </td><td class="response">
 +   <select name="pref_env" size="1">
  
 +.. raw:: html
 +   :file: select_os_options.inc
  
 -General purpose computing
 -~~~~~~~~~~~~~~~~~~~~~~~~~
 +.. raw:: html
  
 -``check boxes``
 +   </select>
 +   </td></tr><tr><td>
  
 -Matlab, R, Python, Octave, ...
 +What **host operating system** are the virtual machines running on?
  
 -``various collections of software for various purposes``
 +.. raw:: html
  
 +   </td><td class="response">
 +   <select name="pref_env" size="1">
  
 -NeuroDebian
 ------------
 +.. raw:: html
 +   :file: select_os_options.inc
  
 -Do you use NeuroDebian repository: ``yes, no``
 +.. raw:: html
  
 -....
 +   </select>
 +   </td></tr><tr><td colspan="2">
  
 +What are your reasons for employing virtualization in you research?
 +Please indicate how much you agree to the following statements.
  
+ Generic computing/scripting/programming environments
+ 
+ C/C++
+ IDL
+ LISREL
+ Maple
+ Mathcad
+ Mathematica
+ Matlab
+ Octave
+ Perl
+ Python
+ R
+ Ruby
+ Scilab
+ SPSS
+ SCIRun
+ Shell scripting
+ 
+ 
+ Distributed Computing - frameworks and controllers
+ 
+ SGE
+ Torque/OpenPBS/Maui
+ Condor
+ Globus
+ MPI (any)
+ IPython
+ 
+ 
+ Imaging
+ 
+ 3D Slicer
+ AFNI
+ Aeskulap
+ Amide
+ BIRN Tools
+ BRAINS Tools
+ Bioimage Suite
+ BrainMap
+ BrainVISA/Anatomist
+ BrainVoyager
+ CMTK
+ Caret
+ ConnectomeViewer
+ DSI Studio
+ DTI-TK
+ Diffusion Toolkit/Trackvis
+ FSL
+ Fiji
+ FreeSurfer
+ ITK/SNAP
+ ImageJ
+ Invesalius
+ LONI
+ Lipsia
+ MIPAV/JIST
+ MRIcron
+ MRtrix
+ Mango
+ NiPy/NiTime/DiPy/NiPype
+ PyMVPA
+ REST
+ SPM
+ V3D
+ VoxBo
+ 
+ Data management
+ 
+ XNAT/PyXNAT/...
+ Human Imaging Database (HID)
+ 
+ Neural Systems Modeling
+ 
+ Brian
+ iqr
+ iNVT
+ NEURON
+ NEST
+ Genesis
+ Moose
+ PCSIM
+ PyNN
+ 
+ Electrophysiology
+ 
+ BioSig
+ BrainStorm
+ Chronus
+ EEGLAB
+ Fieldtrip
+ LORETA/sLORETA
+ OpenMEEG
+ Openelectrophy
+ RTXI
+ Relacs
+ ?Trellis-neuro
+ 
+ Brain-computer interface
+ 
+ BCI2000
+ OpenVIBE
+ Pyff
+ 
+ Hardware interface/Data acquisition
+ 
+ Comedi
+ EPICS
+ MX
+ 
+ Real-time solutions
+ 
+ RTAI
+ Xenomai
+ RTLinux
+ PREEMPT_RT
+ 
+ Psychophysics/Experimental Control
+ 
+ E-Prime
+ Presentation
+ PsychoPy
+ PyEPL
+ Psychtoolbox
+ Psytoolkit
+ OpenSesame
+ VisionEgg
+ Tscope
+ 
+ 
  .. raw:: html
  
 -   <input value="Go" type="button" onclick='JavaScript:xmlhttpPost("/cgi-bin/surveycollector.cgi")'></p>
 +   </td></tr><tr class="oddrow"><td class="task">
 +
 +I can run software that is otherwise incompatible with my system.
 +
 +.. raw:: html
 +
 +   </td><td class="response">
 +   <div class="rating">Definitely agree<br /><input type="radio" name="inst_r1" value="yes" /></div>
 +   <div class="rating">Mostly agree<br /><input type="radio" name="inst_r1" value="yes" /></div>
 +   <div class="rating">Mostly disagree<br /><input type="radio" name="inst_r1" value="yes" /></div>
 +   <div class="rating">Definitely disagree<br /><input type="radio" name="inst_r1" value="yes" /></div>
 +   </td></tr><tr><td class="task">
 +
 +I have the ability to easily create snapshot of my whole analysis environment.
 +
 +.. raw:: html
 +
 +   </td><td class="response">
 +   <div class="rating">Definitely agree<br /><input type="radio" name="inst_r1" value="yes" /></div>
 +   <div class="rating">Mostly agree<br /><input type="radio" name="inst_r1" value="yes" /></div>
 +   <div class="rating">Mostly disagree<br /><input type="radio" name="inst_r1" value="yes" /></div>
 +   <div class="rating">Definitely disagree<br /><input type="radio" name="inst_r1" value="yes" /></div>
 +   </td></tr><tr class="oddrow"><td class="task">
 +
 +
 +I can take my complete analysis environment with me and run in on different
 +machines.
 +
 +.. raw:: html
 +
 +   </td><td class="response">
 +   <div class="rating">Definitely agree<br /><input type="radio" name="inst_r1" value="yes" /></div>
 +   <div class="rating">Mostly agree<br /><input type="radio" name="inst_r1" value="yes" /></div>
 +   <div class="rating">Mostly disagree<br /><input type="radio" name="inst_r1" value="yes" /></div>
 +   <div class="rating">Definitely disagree<br /><input type="radio" name="inst_r1" value="yes" /></div>
 +   </td>
 +   </tr>
 +   </table>
 +
 +
 +Resources for scientific software
 +---------------------------------
 +
 +Where do you obtain scientific software that you employ in your research? Please
 +check all items that apply.
 +
 +.. raw:: html
 +
 +   <table class="questionaire">
 +   <tr class="oddrow">
 +   <td class="response"><input type="checkbox" name="software_resource" value="pet" /></td><td>
 +
 +Directly form vendor or project website
 +
 +.. raw:: html
 +
 +   </td></tr><tr><td class="response"><input type="checkbox" name="software_resource" value="" /></td><td>
 +
 +Retailer
 +
 +.. raw:: html
 +
 +   </td></tr><tr class="oddrow"><td class="response"><input type="checkbox" name="software_resource" value="" /></td><td>
 +
 +`Extra Packages for Enterprise Linux (EPEL) <http://fedoraproject.org/wiki/EPEL>`_
 +
 +.. raw:: html
 +
 +   </td></tr><tr><td class="response"><input type="checkbox" name="software_resource" value="" /></td><td>
 +
 +`Fink <http://www.finkproject.org>`_
 +
 +.. raw:: html
 +
 +   </td></tr><tr class="oddrow"><td class="response"><input type="checkbox" name="software_resource" value="" /></td><td>
 +
 +`FreeBSD ports <http://www.freebsd.org/ports/science.html>`_
 +
 +.. raw:: html
 +
 +   </td></tr><tr><td class="response"><input type="checkbox" name="software_resource" value="" /></td><td>
 +
 +`International neuroinformatics Coordinating Facility (INCF) Research Tools <http://www.incf.org/resources/research-tools>`_
 +
 +.. raw:: html
 +
 +   </td></tr><tr class="oddrow"><td><input type="checkbox" name="software_resource" value="" /></td><td>
 +
 +`Macports <http://www.macports.org>`_
 +
 +.. raw:: html
 +
 +   </td></tr><tr><td class="response"><input type="checkbox" name="software_resource" value="" /></td><td>
 +
 +`NeuroDebian <http://neuro.debian.net>`_
 +
 +.. raw:: html
 +
 +   </td></tr><tr class="oddrow"><td class="response"><input type="checkbox" name="software_resource" value="" /></td><td>
 +
 +`Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) <http://www.nitrc.org>`_
 +
 +.. raw:: html
 +
 +   </td></tr><tr><td class="response"><input type="checkbox" name="software_resource" value="" /></td><td>
 +
 +`Python Package Index (PyPi) <http://pypi.python.org>`_
 +
 +.. raw:: html
 +
 +   </td></tr><tr class="oddrow"><td class="response"><input type="checkbox" name="software_resource" value="" /></td><td>
 +
 +`Sourceforge <http://www.sourceforge.net>`_
 +
 +.. raw:: html
 +
 +   </td></tr><tr><td class="response"><input type="checkbox" name="software_resource" value="other" /></td><td>
 +   <input name="other_resource" type="text" size="40" maxlength="200">
 +   </td></tr></table>
 +
 +Software selection
 +------------------
 +
 +.. raw:: html
 +
 +   <input value="Go" type="button"
 +          onclick='JavaScript:xmlhttpPost("/cgi-bin/surveycollector.cgi")'>
 +
     <div id="result"></div>
     </form>