Re: Summary of discussion from ARO session on "Research and Teaching tools for Matlab" ("Goverts, ST" )

Subject: Re: Summary of discussion from ARO session on "Research and Teaching tools for Matlab" From: "Goverts, ST" <st.goverts@xxxxxxxx> Date: Fri, 11 Mar 2016 13:52:42 +0000 List-Archive:<http://lists.mcgill.ca/scripts/wa.exe?LIST=AUDITORY> --_000_3359B4493D07DC4AAC3E0B5316FB695B69C2BCD7spmxmbx2_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable 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 fo= r. 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 t= he software used to conduct the research is freely available for downloadin= g. However, the latter requires authors to be comfortable sharing their sof= tware at the time of publication. This might be difficult to achieve in ve= ry 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<blocked::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= LL.CA] 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 --- 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 efficien= t sharing of MATLAB tools and resources for research and teaching? This top= ic is motivated by a number of reasons: 1. less duplication of effort across labs & development of teaching reso= urces; 2. rigor and reproducibility of work, especially after graduation of gra= d students; 3. improve learning experience for students; 4. maybe having a more focused location for teaching and research resour= ces may be more useful than just on Google? While a conclusion was not reached during this meeting because of time cons= traints, we had some fruitful discussions and a number of issues were raise= d that should be the focus of future sessions. Most of the discussion revol= ved 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 MATL= AB 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 pract= ices, and (2) open issues. 1. Possible best practices for sharing * Post code online freely, rather than only providing when asked. Facil= itates access, especially by students. * Tagging - using meaningful keywords for code posted on the internet s= o that it is easier to search with internet search engines. * Being motivated to share code before the start of the project. This c= an lead to better coding and documentation. * Sharing of code should include simple usage examples, data sets and p= erhaps be able to generate figures within publications by the authors. 2. Open issues * Posting on Auditory list may be initially good for announcing availab= ility but may not be easy to find beyond initial announcement. Using tags a= nd meaningful keywords may facilitate searchability of code. * When searching online for tools, sometimes it is difficult to know wh= at 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 ex= amples 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 o= n 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 availa= ble within MATLAB to facilitate sharing; as well as what other communities = are doing to share teaching resources. --_000_3359B4493D07DC4AAC3E0B5316FB695B69C2BCD7spmxmbx2_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable <html xmlns:v=3D"urn:schemas-microsoft-com:vml" xmlns:o=3D"urn:schemas-micr= osoft-com:office:office" xmlns:w=3D"urn:schemas-microsoft-com:office:word" = xmlns:m=3D"http://schemas.microsoft.com/office/2004/12/omml" xmlns=3D"http:= //www.w3.org/TR/REC-html40"> <head> <meta http-equiv=3D"Content-Type" content=3D"text/html; charset=3Dus-ascii"= > <meta name=3D"Generator" content=3D"Microsoft Word 14 (filtered medium)"> <style></style> </head> <body lang=3D"NL" link=3D"#0563C1" vlink=3D"#954F72"> <div class=3D"WordSection1"> Dear coll= egues<o:p></o:p> <o:p>&nbs= p;</o:p> A short n= ote in addition to this discussion.<o:p></o:p> We feel t= he most effective way to promote better sharing of software is to make a st= rong 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 piec= e of software  if he or she can see which articles were based on it.&n= bsp; 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 th= e time of publication.  This might be difficult to achieve in very com= petitive fields of research. <o:p></o:p> <o:p>&nbs= p;</o:p> Regards,<= o:p></o:p> <o:p>&nbs= p;</o:p> Lucas Sta= m and Theo Goverts, <o:p></o:p> VU University Medical Ce= nter, AMSTERDAM<o:p></o:p> <o:p> </o:p></spa= n> <o:p> </o:p></spa= n> S.Theo Goverts PhD medical physicist audiologist, head of University Audiological Center</span= ><o:p></o:p>  <o= :p></o:p> Dept. of Otolaryngology-Head and Neck Surgery, section Ear &= amp; Hearing <o:p></o:p> EMGO Institute for Health and Care Research<o:p></o:p> = E: <a href=3D"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 Netherl= ands<o:p></o:p> <o:p> </o:p> <a href=3D"htt= p://www.ac-vumc.nl/">www.ac-vumc.nl</a> <a href=3D"http://www.ci-vumc.n/">www.ci-vumc.n</a>l <a href=3D"http://www.lhca.nl/">www.lhca.nl</a><o:p></o:p> <a href=3D"blo= cked::www.vumc.nl">www.vumc.nl</a> <a href=3D"http://www.vumc.nl/socialemedia">www.vumc.nl/socialemedia</= a> <a href=3D"http://www.vumc.nl/steun-ons">www.vumc.nl/steun-ons</a></sp= an> <o:p></o:p> <o:p> </o:p> <o:p>&n= bsp;</o:p> <o:p>&n= bsp;</o:p> <o:p>&n= bsp;</o:p> <div> <div style=3D"border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm = 0cm 0cm"> Van: AUDITORY - Research in Auditory Perception [<sp= an style=3D"font-size:10.0pt;font-family:"Tahoma","sans-seri= f""><a href=3D"mailto:AUDITORY@xxxxxxxx">m= ailto:AUDITORY@xxxxxxxx</a>] Namens Alan Kan Verzonden: vrijdag 4 maart 2016 1:14 Aan: <a href=3D"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></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 w= ell. <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></sp= an> 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=3D"http://www.waisman.wisc.edu/~ahkan">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 R= esearch and Teaching Tools for MATLAB was to try and answer the question: What are the community needs for the efficient sharing of MATLAB tools a= nd resources for research and teaching? This topic is motivated by a nu= mber of reasons:<o:p></o:p></p= > <ol style=3D"margin-top:0cm" start=3D"1" type=3D"1"> <li class=3D"MsoNormal" style=3D"color:black;mso-list:l3 level1 lfo3;vertic= al-align:baseline"> less duplication of effort across labs & development of teachi= ng resources;<o:p></o:p></li><li class=3D"MsoNormal" style=3D"color:= black;mso-list:l3 level1 lfo3;vertical-align:baseline"> rigor and reproducibility of work, especially after graduation of = grad students;<o:p></o:p></li><li class=3D"MsoNormal" style=3D"color= :black;mso-list:l3 level1 lfo3;vertical-align:baseline"> improve learning experience for students;<o:p></o:p></li><l= i class=3D"MsoNormal" style=3D"color:black;mso-list:l3 level1 lfo3;vertical= -align:baseline"> maybe having a more focused location for teaching and research res= ources may be more useful than just on Google?<o:p></o:p></li></ol> <o:p> </o:p></sp= an> While a conclusion was not reac= hed during this meeting because of time constraints, we had some fruitful d= iscussions and a number of issues were raised that should be the focus of future sessions. Most of the discussion revolved around th= e sharing of research tools. There was brief mention of a web-based textboo= k for teaching of MATLAB and/or for hearing sciences with MATLAB code examp= les. 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></sp= an> The following summary is divide= d into two sections: (1) possible best practices, and (2) open issues. <o:p></o:p> <o:p> </o:p></sp= an> 1. Possible best practices f= or sharing<o:p></o:p> <ul style=3D"margin-top:0cm" type=3D"disc"> <li class=3D"MsoNormal" style=3D"color:black;mso-list:l2 level1 lfo6;vertic= al-align:baseline"> Post code online freely, rather than only providing when asked. Fa= cilitates access, especially by students. <o:p></o:p></li><li class=3D"MsoNormal" style=3D"color:black;mso-lis= t:l2 level1 lfo6;vertical-align:baseline"> Tagging - using meaningful keywords for code posted on the interne= t so that it is easier to search with internet search engines.<o:p></o:p></= span></li><li class=3D"MsoNormal" style=3D"color:black;mso-list:l2 level1 l= fo6;vertical-align:baseline"> Being motivated to share code before the start of the project. Thi= s can lead to better coding and documentation.<o:p></o:p></li><li cl= ass=3D"MsoNormal" style=3D"color:black;mso-list:l2 level1 lfo6;vertical-ali= gn:baseline"> Sharing of code should include simple usage examples, data sets an= d perhaps be able to generate figures within publications by the authors.<o= :p></o:p></li></ul> <o:p> </o:p></sp= an> 2. Open issues<sp= an lang=3D"EN-US" style=3D"font-size:12.0pt;font-family:"Times New Rom= an","serif""><o:p></o:p> <ul style=3D"margin-top:0cm" type=3D"disc"> <li class=3D"MsoNormal" style=3D"color:black;mso-list:l4 level1 lfo9;vertic= al-align:baseline"> Posting on Auditory list may be initially good for announcing avai= lability but may not be easy to find beyond initial announcement. Using tag= s and meaningful keywords may facilitate searchability of code. <o:p></o:p></li><li class=3D"MsoNormal" style=3D"color:black;= mso-list:l4 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=3D"MsoNormal" style=3D"color:black;mso-lis= t:l4 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=3D"MsoNormal" style= =3D"color:black;mso-list:l4 level1 lfo9;vertical-align:baseline"> Liability - who is liable? Licensing issues was briefly discussed.= <o:p></o:p></li><li class=3D"MsoNormal" style=3D"color:black;mso-lis= t:l4 level1 lfo9;vertical-align:baseline"> Sharing of datasets and speech corpuses. <o:p></o:p></li></ul> <o:p> </o:p></sp= an> The slides from presentations b= y Alan Kan, Michael Heinz, Ray Goldsworthy, Denis Drennan, Piotr Madjak, La= urel 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; w= hat tools are currently being shared; what tools are available within MATLA= B to facilitate sharing; as well as what other communities are doing to share teaching resources. <s= pan lang=3D"EN-US" style=3D"font-size:12.0pt;font-family:"Times New Ro= man","serif""><o:p></o:p> <o:p> </o:p> </div> </body> </html> --_000_3359B4493D07DC4AAC3E0B5316FB695B69C2BCD7spmxmbx2_--

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