-Computing environments in neuroscience research
-===============================================
+Scientific software usage in neuroscience research
+==================================================
.. raw:: html
}
</script>
-General
--------
+ <form name="nss_survey" enctype="application/x-www-form-urlencoded">
-Subfield of neuroscience: ``MRI, EEG, MEG, electrophys. ...``
-Position: ``undergraduate, phd student, postdoc, professor/supervisor, sysadmin``
-employer: ``higher education (private/public funding), research facility
-(private/public funding, company)``
-country: ``long list``
-do you develop software intended to be used by other researchers: ``yes, no``
+Personal background
+-------------------
-Personal computing environment
-------------------------------
+.. raw:: html
+
+ <table>
+ <tr class="oddrow">
+ <td>
+
+Which country are working in?
+
+.. raw:: html
+
+ </td><td class="response">
+
+.. raw:: html
+ :file: select_country.inc
+
+.. raw:: html
+
+ </td></tr><tr><td>
+
+Where are you working?
+
+.. raw:: html
+
+ </td><td class="response">
+ <select name="position" size="1">
+ <option value="none" selected="selected" label="Select an option"></option>
+ <option value="edu_priv" label="Higher education (privately funded)"></option>
+ <option value="edu_pub" label="Higher education (publicly funded)"></option>
+ <option value="research_priv" label="Research institution (privately funded)"></option>
+ <option value="research_pub" label="Research institution (publicly funded)"></option>
+ <option value="company" label="Company"></option>
+ </select>
+ </td></tr><tr class="oddrow"><td>
+
+What is your position?
+
+.. raw:: html
+
+ </td><td class="response">
+ <select name="position" size="1">
+ <option value="none" selected="selected" label="Select an option"></option>
+ <option value="undergrad" label="Undergraduate student"></option>
+ <option value="graduate" label="PhD student"></option>
+ <option value="postdoc" label="Postdoc"></option>
+ <option value="professor" label="Professor/Supervisor"></option>
+ <option value="ra" label="Research assistant"></option>
+ <option value="researcher" label="Other researcher"></option>
+ <option value="sysadmin" label="System administrator"></option>
+ </select>
+ </td></tr><tr><td>
+
+What type of data are you working with? Please check all items that apply.
+
+.. raw:: html
+
+ </td><td class="response">
+ <table><tr><td>
+ <input type="checkbox" name="datamod" value="behav" />Behavioral<br />
+ <input type="checkbox" name="datamod" value="mri" />MRI/fMRI/DTI<br />
+ <input type="checkbox" name="datamod" value="meeg" />EEG/MEG<br />
+ </td><td>
+ <input type="checkbox" name="datamod" value="pet" />PET/SPECT<br />
+ <input type="checkbox" name="datamod" value="ephys" />Electrophysiology<br />
+ <input type="checkbox" name="datamod" value="spectro" />Microspectroscopy<br />
+ <input type="checkbox" name="datamod" value="other" />
+ <input name="other_datamodality" type="text" size="20" maxlength="40">
+ </td></tr></table>
+ </td></tr><tr class="oddrow"><td>
+
+Are you developing software that is intended to be used by other researchers?
+
+.. raw:: html
+
+ </td><td class="response">
+ <span><input type="radio" name="developer" value="yes" />Yes</span>
+ <span><input type="radio" name="developer" value="no" checked="checked" />No</span>
+ </td>
+ </tr>
+ </table>
+
+Personal scientific software environment
+----------------------------------------
+
+Here are a few questions about your personal scientific software environment
+for research activities like data acquisition, computational modeling, and data
+analysis. You might be running this on your laptop, desktop, personal
+workstation or any other machine where **you decide** what software you are
+using, and you typically also have permission to **install it yourself**. If
+you are operating different environments, please describe the one that you find
+most productive for your research purposes. If you don't have a machine that
+you administer yourself, instead, please indicate what kind of scientific
+software environment you would like to be doing your research in.
+
+.. raw:: html
+
+ <table>
+ <tr>
+ <td>
+
+What type of hardware are you using?
+
+.. raw:: html
+
+ </td><td class="response">
+ <select name="pref_env" size="1">
+ <option value="none" selected="selected" label="Select an option"></option>
+ <option value="laptop" label="Laptop/Portable device"></option>
+ <option value="desktop" label="Commodity desktop"></option>
+ <option value="workstation" label="High-performance workstation"></option>
+ <option value="cluster" label="Compute cluster"></option>
+ <option value="grid" label="Grid/Cloud-computing facility"></option>
+ </select>
+ </td></tr><tr><td>
+
+What operating system is this environment running on?
+
+.. raw:: html
+
+ </td><td class="response">
+ <select name="pref_env" size="1">
+
+.. raw:: html
+ :file: select_os_options.inc
+
+.. raw:: html
+
+ </select>
+ </td></tr><tr><td>
+
+What fraction of your research activity time do you spend in this software
+environment as opposed to any other environment that you migh have access to?
+
+.. raw:: html
+
+ </td><td class="response">
+ <select name="pref_time" size="1">
+ <option value="none" selected="selected" label="Select an option"></option>
+ <option value="notime" label="None/I don't have this environment"></option>
+ <option value="little" label="Less then half of the time"></option>
+ <option value="most" label="More than half of the time"></option>
+ <option value="always" label="All of the time"></option>
+ </select>
+ </td></tr><tr><td>
+
+How much time do you spend each month on maintaining this environment? This
+includes the time spent on operating system (security) upgrades, as well as
+installing and updating scientific software.
+
+.. raw:: html
+
+ </td><td class="response">
+ <input name="maint_time" type="text" size="3" maxlength="3"> hours per month
+ </td>
+ </tr>
+ </table>
+
+---------------------------------------------------------------
+
+Please indicate how much you agree to the following statements.
+
+.. raw:: html
+
+ <table>
+ <tr><th colspan="2" style="text-align:left;font-weight:normal">
+
+*I prefer this particular scientific software environment because ...*
+
+.. raw:: html
+
+ </th></tr><tr class="oddrow">
+ <td class="task">
+
+... the developers of an important research software recommend it
+
+.. 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">
+
+
+... of the variety of available research software for this 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">
+
+
+... of the availibility of commercial support
+
+.. 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">
+
+
+... many of my colleagues use something similar
+
+.. 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">
+
+
+... it is popular and I can get solutions for problems from web forums and mailing lists
+
+.. 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 rely on an particular application that only runs in this 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">
+
+
+... it has adequate support for all required hardware
+
+.. 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 necessary technical skills to maintain this environment myself
+
+.. 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>
+
+
+Managed scientific software environment
+---------------------------------------
+
+The following questions are about a managed environment of scientific software
+that is provided to you to carry out computing and data analysis related
+research activities. Such an environment is typically managed by **dedicated IT
+staff**, and **you don't have permissions to install arbitrary software**. This
+environment may be shared by many researchers in a lab, a whole research
+institution, or even be publicly accessible. If you have access to multiple
+environments of this kind, please describe the one that offers most support for
+your particular research purposes.
+
+
+.. raw:: html
+
+ <table class="questionaire">
+ <tr>
+ <td>
+
+What type of hardware is this software environment running on?
+
+.. raw:: html
-Here are a few questions about your preferred computing environment for
-research activities like data acquisition and data analysis. This might be your
-laptop, desktop, personal workstation or any other machine where **you decide**
-what software you are using, and you have permission to install it yourself.
-If you are using multiple environment, please describe the one that you find
-most productive for research purposes. If you don't have access to a machine
-for research purposes that you administer yourself, instead, please indicate
-what kind of environment you would like to be doing your research in.
+ </td><td class="response">
+ <select name="pref_env" size="1">
+ <option value="none" selected="selected" label="Select an option"></option>
+ <option value="laptop" label="Laptop/Portable device"></option>
+ <option value="desktop" label="Commodity desktop"></option>
+ <option value="workstation" label="High-performance workstation"></option>
+ <option value="cluster" label="Compute cluster"></option>
+ <option value="grid" label="Grid/Cloud-computing facility"></option>
+ </select>
+ </td></tr><tr><td>
-Do you have it: ``yes, no``
-Type: ``laptop, commodity desktop, dedicated workstation,
-compute cluster, grid/cloud computing environment``
+What operating system is this environment running on?
-Operating system: ``detailed choice, long list``
+.. raw:: html
+
+ </td><td class="response">
+ <select name="pref_env" size="1">
+
+.. raw:: html
+ :file: select_os_options.inc
+
+.. raw:: html
+
+ </select>
+ </td></tr><tr><td>
-I prefer this environment because is offers (check all items that apply):
+What fraction of time do you spend in this environment during your research
+activities?
-``checkboxes (variety of available software; hardware support; ...)``
+.. raw:: html
+
+ </td><td class="response">
+ <select name="pref_time" size="1">
+ <option value="none" selected="selected" label="Select an option"></option>
+ <option value="notime" label="None/I don't use this"></option>
+ <option value="little" label="Less then half of the time"></option>
+ <option value="most" label="More than half of the time"></option>
+ <option value="always" label="All of the time"></option>
+ </select>
+ </td>
+ </tr>
+ </table>
+---------------------------------------------------------------
-Institutionally provided computing environment
-----------------------------------------------
+How much do you agree to the following statements?
-The following questions are about
-What your employer offers.
+.. raw:: html
-Do you use it: ``yes, no``
+ <table>
+ <tr class="oddrow">
+ <td class="task">
-Type: ``laptop, commodity desktop, dedicated workstation,
-compute cluster, grid/cloud computing environment``
+This environment provides me with the best available tools for my research.
-Operating system: ``detailed choice, long list``
+.. raw:: html
-I dislike (check all items that apply):
+ </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">
+
+The support staff solves all my technical problems and addresses my demands in
+a timely fashion.
+
+.. 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">
+
+There are always enough licenses for essential commerical software tools.
+
+.. 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 need to deploy additional software to be able to perform my research in this 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">
+
+
+Using this managed environment is more cost effective than operating a suitable
+environment myself.
+
+.. raw:: html
-``checkboxes (limited set of available software; slow admin response; ...)``
+ </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">
+.. raw:: html
+ </td>
+ </tr>
+ </table>
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
.. 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>
-Thanks
+
projects / neurodebian.git / blobdiff