Re: Summary of discussion from ARO session on "Research and Teaching tools for Matlab" (Alan Kan )

Subject: Re: Summary of discussion from ARO session on "Research and Teaching tools for Matlab" From: Alan Kan <alan.kan@xxxxxxxx> Date: Thu, 17 Mar 2016 14:54:02 +0000 List-Archive:<http://lists.mcgill.ca/scripts/wa.exe?LIST=AUDITORY> --Boundary_(ID_fFwNCndKiV7KIrsEnyL/6A) Content-type: text/plain; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Hi Marcus, I was not aware of this development but taking a brief wander on the site, it looks pretty interesting. I am going to have to explore it some more, sometime! Thanks for the heads up. Cheers Alan From: AUDITORY - Research in Auditory Perception [mailto:AUDITORY@xxxxxxxx On Behalf Of Marcus Pearce Sent: Wednesday, March 16, 2016 9:39 AM To: AUDITORY@xxxxxxxx Subject: Re: [AUDITORY] Summary of discussion from ARO session on "Research and Teaching tools for Matlab" Dear All, Thanks for the summary, it seems relevant to mention the SoundSoftware project here: https://code.soundsoftware.ac.uk/ This is a software development and publishing platform for research on sound & music processing. The purpose is to support sustainable development of research software and, with particular reference to Lucas and Theo's message below, it allows you to associate articles and other publications with the software. It also provides projects with options including a wiki, a version control repository, facilities for listing members, creating downloads and other functionality. Marcus -- Senior Lecturer in Sound and Music Processing Queen Mary, University of London Mile End Road, London E1 4NS, UK Tel: +44 (0)20 7882 6207 Web: http://webprojects.eecs.qmul.ac.uk/marcusp Lab: http://music-cognition.eecs.qmul.ac.uk/ On 11/03/2016 13:52, Goverts, ST wrote: Dear collegues A short note in addition to this discussion. We feel the most effective way to promote better sharing of software is to make a strong link between software and the articles/research it is used for. We expect that someone browsing through a software database or website is much more likely to recognize the utility of a piece of software if he or she can see which articles were based on it. It would probably be even more efficient if journal articles included a link to a database in which the software used to conduct the research is freely available for downloading. However, the latter requires authors to be comfortable sharing their software at the time of publication. This might be difficult to achieve in very competitive fields of research. Regards, Lucas Stam and Theo Goverts, VU University Medical Center, AMSTERDAM S.Theo Goverts PhD medical physicist audiologist, head of University Audiological Center Dept. of Otolaryngology-Head and Neck Surgery, section Ear & Hearing EMGO Institute for Health and Care Research E: st.goverts@xxxxxxxx<mailto:st.goverts@xxxxxxxx> T: 020-4440969 De Boelelaan 1118 (PK, 2Y160), 1081 HZ Amsterdam, The Netherlands Postal address: P.O.Box 7057, 1007 MB Amsterdam, The Netherlands www.ac-vumc.nl<http://www.ac-vumc.nl> www.ci-vumc.n<http://www.ci-vumc.n>l www.lhca.nl<http://www.lhca.nl> www.vumc.nl<http://www.vumc.nl> www.vumc.nl/socialemedia<http://www.vumc.nl/socialemedia> www.vumc.nl/steun-ons<http://www.vumc.nl/steun-ons> Van: AUDITORY - Research in Auditory Perception [mailto:AUDITORY@xxxxxxxx Namens Alan Kan Verzonden: vrijdag 4 maart 2016 1:14 Aan: AUDITORY@xxxxxxxx<mailto:AUDITORY@xxxxxxxx> Onderwerp: Summary of discussion from ARO session on "Research and Teaching tools for Matlab" Dear list, A request was made to provide a summary of the discussions that occurred at the session on "Research and Teaching tools for Matlab" at the ARO meeting last week. A summary is provided below. Hopefully it will also spark some interesting discussions among the community of the auditory list as well. Cheers Alan -- Alan Kan, PhD Assistant Scientist | Binaural Hearing and Speech Laboratory University of Wisconsin-Madison Room 563, Waisman Center / 1500 Highland Avenue / Madison, WI, 53705 Phone: +1-608-262-7483 / Fax: +1-608-263-2918 Web: http://www.waisman.wisc.edu/~ahkan<http://www.waisman.wisc.edu/%7Eahkan> --- RESEARCH AND TEACHING TOOLS FOR MATLAB: A COMMUNITY DISCUSSION ARO 2016 The purpose of the session on Research and Teaching Tools for MATLAB was to try and answer the question: What are the community needs for the efficient sharing of MATLAB tools and resources for research and teaching? This topic is motivated by a number of reasons: 1. less duplication of effort across labs & development of teaching resources; 2. rigor and reproducibility of work, especially after graduation of grad students; 3. improve learning experience for students; 4. maybe having a more focused location for teaching and research resources may be more useful than just on Google? While a conclusion was not reached during this meeting because of time constraints, we had some fruitful discussions and a number of issues were raised that should be the focus of future sessions. Most of the discussion revolved around the sharing of research tools. There was brief mention of a web-based textbook for teaching of MATLAB and/or for hearing sciences with MATLAB code examples. Perhaps the ARO website may be a good starting point for hosting this textbook, as well as a place to share research tools? The following summary is divided into two sections: (1) possible best practices, and (2) open issues. 1. Possible best practices for sharing * Post code online freely, rather than only providing when asked. Facilitates access, especially by students. * Tagging - using meaningful keywords for code posted on the internet so that it is easier to search with internet search engines. * Being motivated to share code before the start of the project. This can lead to better coding and documentation. * Sharing of code should include simple usage examples, data sets and perhaps be able to generate figures within publications by the authors. 2. Open issues * Posting on Auditory list may be initially good for announcing availability but may not be easy to find beyond initial announcement. Using tags and meaningful keywords may facilitate searchability of code. * When searching online for tools, sometimes it is difficult to know what to search for. MATLAB answers forum may be a good start. * How do we know if posted code works? Or does what it claims? Usage examples would help. * Liability - who is liable? Licensing issues was briefly discussed. * Sharing of datasets and speech corpuses. The slides from presentations by Alan Kan, Michael Heinz, Ray Goldsworthy, Denis Drennan, Piotr Madjak, Laurel Carney and Lisa Kempler are available on request. These presentations highlight the purpose and reasons for these discussions; how MATLAB is being used for research and teaching within the ARO community; what tools are currently being shared; what tools are available within MATLAB to facilitate sharing; as well as what other communities are doing to share teaching resources. --Boundary_(ID_fFwNCndKiV7KIrsEnyL/6A) Content-type: text/html; CHARSET=US-ASCII Content-transfer-encoding: 7BIT <html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"> <head> <meta http-equiv="Content-Type" content="text/html; charset=us-ascii"> <meta name="Generator" content="Microsoft Word 15 (filtered medium)"> <style></style> </head> <body bgcolor="white" lang="EN-US" link="#0563C1" vlink="#954F72"> <div class="WordSection1"> Hi Marcus,<o:p></o:p> <o:p> </o:p> I was not aware of this development but taking a brief wander on the site, it looks pretty interesting. I am going to have to explore it some more, sometime! Thanks for the heads up.<o:p></o:p> <o:p> </o:p> Cheers<o:p></o:p> <o:p> </o:p> Alan<o:p></o:p> <o:p> </o:p> <div> <div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in"> From: AUDITORY - Research in Auditory Perception [mailto:AUDITORY@xxxxxxxx On Behalf Of Marcus Pearce Sent: Wednesday, March 16, 2016 9:39 AM To: AUDITORY@xxxxxxxx Subject: Re: [AUDITORY] Summary of discussion from ARO session on "Research and Teaching tools for Matlab"<o:p></o:p> </div> </div> <o:p> </o:p> Dear All, Thanks for the summary, it seems relevant to mention the SoundSoftware project here: <a href="https://code.soundsoftware.ac.uk/">https://code.soundsoftware.ac.uk/</a> This is a software development and publishing platform for research on sound & music processing. The purpose is to support sustainable development of research software and, with particular reference to Lucas and Theo's message below, it allows you to associate articles and other publications with the software. It also provides projects with options including a wiki, a version control repository, facilities for listing members, creating downloads and other functionality. Marcus <o:p></o:p> <pre>-- <o:p></o:p></pre> <pre>Senior Lecturer in Sound and Music Processing<o:p></o:p></pre> <pre>Queen Mary, University of London<o:p></o:p></pre> <pre>Mile End Road, London E1 4NS, UK<o:p></o:p></pre> <pre>Tel: +44 (0)20 7882 6207<o:p></o:p></pre> <pre>Web: <a href="http://webprojects.eecs.qmul.ac.uk/marcusp">http://webprojects.eecs.qmul.ac.uk/marcusp</a><o:p></o:p></pre> <pre>Lab: <a href="http://music-cognition.eecs.qmul.ac.uk/">http://music-cognition.eecs.qmul.ac.uk/</a><o:p></o:p></pre> <div> On 11/03/2016 13:52, Goverts, ST wrote:<o:p></o:p> </div> <blockquote style="margin-top:5.0pt;margin-bottom:5.0pt"> Dear collegues<o:p></o:p>  <o:p></o:p> A short note in addition to this discussion.<o:p></o:p> We feel the most effective way to promote better sharing of software is to make a strong link between software and the articles/research it is used for.  We expect that someone browsing through a software database or website is much more likely to recognize the utility of a piece of software  if he or she can see which articles were based on it.  It would probably be even more efficient if journal articles included a link to a database in which the software used to conduct the research is freely available for downloading. However, the latter requires authors to be comfortable sharing their software at the time of publication.  This might be difficult to achieve in very competitive fields of research. <o:p></o:p>  <o:p></o:p> Regards,<o:p></o:p>  <o:p></o:p> Lucas Stam and Theo Goverts, <o:p></o:p> VU University Medical Center, AMSTERDAM<o:p></o:p>  <o:p></o:p>  <o:p></o:p> S.Theo Goverts PhD medical physicist audiologist, head of University Audiological Center<o:p></o:p>  <o:p></o:p> Dept. of Otolaryngology-Head and Neck Surgery, section Ear & Hearing <o:p></o:p> EMGO Institute for Health and Care Research<o:p></o:p> E: <a href="mailto:st.goverts@xxxxxxxx">st.goverts@xxxxxxxx</a><o:p></o:p> T: 020-4440969<o:p></o:p>  <o:p></o:p> De Boelelaan 1118 (PK, 2Y160), 1081 HZ Amsterdam, The Netherlands<o:p></o:p> Postal address: P.O.Box 7057, 1007 MB Amsterdam, The Netherlands<o:p></o:p>  <o:p></o:p> <a href="http://www.ac-vumc.nl">www.ac-vumc.nl</a> <a href="http://www.ci-vumc.n">www.ci-vumc.n</a>l <a href="http://www.lhca.nl">www.lhca.nl</a><o:p></o:p> <a href="http://www.vumc.nl">www.vumc.nl</a> <a href="http://www.vumc.nl/socialemedia">www.vumc.nl/socialemedia</a> <a href="http://www.vumc.nl/steun-ons">www.vumc.nl/steun-ons</a> <o:p></o:p>  <o:p></o:p>  <o:p></o:p>  <o:p></o:p>  <o:p></o:p> <div> <div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in"> Van: AUDITORY - Research in Auditory Perception [<a href="mailto:AUDITORY@xxxxxxxx">mailto:AUDITORY@xxxxxxxx</a>] Namens Alan Kan Verzonden: vrijdag 4 maart 2016 1:14 Aan: <a href="mailto:AUDITORY@xxxxxxxx">AUDITORY@xxxxxxxx</a> Onderwerp: Summary of discussion from ARO session on "Research and Teaching tools for Matlab"<o:p></o:p> </div> </div>  <o:p></o:p> Dear list,<o:p></o:p>  <o:p></o:p> A request was made to provide a summary of the discussions that occurred at the session on "Research and Teaching tools for Matlab" at the ARO meeting last week. A summary is provided below. Hopefully it will also spark some interesting discussions among the community of the auditory list as well. <o:p></o:p>  <o:p></o:p> Cheers<o:p></o:p>  <o:p></o:p> Alan<o:p></o:p>  <o:p></o:p> -- Alan Kan, PhD Assistant Scientist | Binaural Hearing and Speech Laboratory<o:p></o:p> University of Wisconsin-Madison Room 563, Waisman Center / 1500 Highland Avenue / Madison, WI, 53705 Phone: +1-608-262-7483 / Fax: +1-608-263-2918 Web: <a href="http://www.waisman.wisc.edu/%7Eahkan">http://www.waisman.wisc.edu/~ahkan</a><o:p></o:p> ---<o:p></o:p>  <o:p></o:p> RESEARCH AND TEACHING TOOLS FOR MATLAB: A COMMUNITY DISCUSSION<o:p></o:p> ARO 2016<o:p></o:p>  <o:p></o:p> The purpose of the session on Research and Teaching Tools for MATLAB was to try and answer the question: What are the community needs for the efficient sharing of MATLAB tools and resources for research and teaching? This topic is motivated by a number of reasons:<o:p></o:p> <ol style="margin-top:0in" start="1" type="1"> <li class="MsoNormal" style="mso-list:l2 level1 lfo3;vertical-align:baseline">less duplication of effort across labs & development of teaching resources;<o:p></o:p></li><li class="MsoNormal" style="mso-list:l2 level1 lfo3;vertical-align:baseline">rigor and reproducibility of work, especially after graduation of grad students;<o:p></o:p></li><li class="MsoNormal" style="mso-list:l2 level1 lfo3;vertical-align:baseline">improve learning experience for students;<o:p></o:p></li><li class="MsoNormal" style="mso-list:l2 level1 lfo3;vertical-align:baseline">maybe having a more focused location for teaching and research resources may be more useful than just on Google?<o:p></o:p></li></ol>  <o:p></o:p> While a conclusion was not reached during this meeting because of time constraints, we had some fruitful discussions and a number of issues were raised that should be the focus of future sessions. Most of the discussion revolved around the sharing of research tools. There was brief mention of a web-based textbook for teaching of MATLAB and/or for hearing sciences with MATLAB code examples. Perhaps the ARO website may be a good starting point for hosting this textbook, as well as a place to share research tools? <o:p></o:p>  <o:p></o:p> The following summary is divided into two sections: (1) possible best practices, and (2) open issues. <o:p></o:p>  <o:p></o:p> 1. Possible best practices for sharing<o:p></o:p> <ul style="margin-top:0in" type="disc"> <li class="MsoNormal" style="mso-list:l1 level1 lfo6;vertical-align:baseline">Post code online freely, rather than only providing when asked. Facilitates access, especially by students. <o:p></o:p></li><li class="MsoNormal" style="mso-list:l1 level1 lfo6;vertical-align:baseline">Tagging - using meaningful keywords for code posted on the internet so that it is easier to search with internet search engines.<o:p></o:p></li><li class="MsoNormal" style="mso-list:l1 level1 lfo6;vertical-align:baseline">Being motivated to share code before the start of the project. This can lead to better coding and documentation.<o:p></o:p></li><li class="MsoNormal" style="mso-list:l1 level1 lfo6;vertical-align:baseline">Sharing of code should include simple usage examples, data sets and perhaps be able to generate figures within publications by the authors.<o:p></o:p></li></ul>  <o:p></o:p> 2. Open issues<o:p></o:p> <ul style="margin-top:0in" type="disc"> <li class="MsoNormal" style="mso-list:l3 level1 lfo9;vertical-align:baseline">Posting on Auditory list may be initially good for announcing availability but may not be easy to find beyond initial announcement. Using tags and meaningful keywords may facilitate searchability of code. <o:p></o:p></li><li class="MsoNormal" style="mso-list:l3 level1 lfo9;vertical-align:baseline">When searching online for tools, sometimes it is difficult to know what to search for. MATLAB answers forum may be a good start. <o:p></o:p></li><li class="MsoNormal" style="mso-list:l3 level1 lfo9;vertical-align:baseline">How do we know if posted code works? Or does what it claims? Usage examples would help.<o:p></o:p></li><li class="MsoNormal" style="mso-list:l3 level1 lfo9;vertical-align:baseline">Liability - who is liable? Licensing issues was briefly discussed.<o:p></o:p></li><li class="MsoNormal" style="mso-list:l3 level1 lfo9;vertical-align:baseline">Sharing of datasets and speech corpuses. <o:p></o:p></li></ul>  <o:p></o:p> The slides from presentations by Alan Kan, Michael Heinz, Ray Goldsworthy, Denis Drennan, Piotr Madjak, Laurel Carney and Lisa Kempler are available on request. These presentations highlight the purpose and reasons for these discussions; how MATLAB is being used for research and teaching within the ARO community; what tools are currently being shared; what tools are available within MATLAB to facilitate sharing; as well as what other communities are doing to share teaching resources. <o:p></o:p>  <o:p></o:p> </blockquote> </div> </body> </html> --Boundary_(ID_fFwNCndKiV7KIrsEnyL/6A)--

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