Re: [Bioc-devel] Use and Usability metrics / shields
Awesome! Here's the code in case others want to add the shields to their github readme files. https://gist.github.com/lcolladotor/de2e0b67fbf33518b922 derfinder example (software package) https://github.com/lcolladotor/derfinder derfinderData example (experiment data package) https://github.com/leekgroup/derfinderData On Fri, Jun 12, 2015 at 12:32 AM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Leonardo Collado Torres lcoll...@jhu.edu To: Dan Tenenbaum dtene...@fredhutch.org Cc: bioc-devel@r-project.org Sent: Thursday, June 11, 2015 9:26:13 PM Subject: Re: [Bioc-devel] Use and Usability metrics / shields Is it ok if we use the Bioconductor shields elsewhere? For example, in a github repo landing page or in our website listing the software we've contributed to. In particular, I'm thinking of adding http://www.bioconductor.org/shields/posts/derfinder.svg (and the other shields) to https://github.com/lcolladotor/derfinder to go along the Travis CI shield I use right now. Feel free, that was part of the idea. Dan On Thu, Jun 4, 2015 at 11:22 AM, Jim Hester james.f.hes...@gmail.com wrote: Henrik, While I proposed the idea for the shields/badges Dan gets all the credit for the implementation. As far as your (implied) idea of a coverage badge, the thought had occurred to us! Jim On Wed, May 20, 2015 at 1:34 PM, Henrik Bengtsson henrik.bengts...@ucsf.edu wrote: So, lots of things are happening in a few months: Jim Hester starts working at Bioconductor, we get Bioc shields/badges, Jim's covr package is released on CRAN, snare drum, ... am I to eager if I already now start wishing for a hi-hat as well? /Henrik On Tue, May 19, 2015 at 12:47 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Leonardo Collado Torres lcoll...@jhu.edu To: Dan Tenenbaum dtene...@fredhutch.org Cc: Jim Hester james.f.hes...@gmail.com, bioc-devel@r-project.org Sent: Tuesday, May 19, 2015 12:37:18 PM Subject: Re: [Bioc-devel] Use and Usability metrics / shields Regarding the 'posts' tag, I can see that it includes a closed questions component. For example, http://www.bioconductor.org/packages/release/bioc/html/derfinder.html is 3/1/9/0 right now meaning that 0 questions are closed. From https://support.bioconductor.org/info/faq/, only moderators can close questions. That seems like quite a bit of work for the moderators. So maybe it would be best to drop the closed questions component. Or alternatively, can the author of a package moderate the posts that have a tag corresponding to their package? Perhaps the wording is wrong; what 'closed' is supposed to mean is that the original poster has accepted an answer. I'll change 'closed' to 'accepted'. As for 'build: warnings', it seems like it will show for some devel packages all the time. For example, http://www.bioconductor.org/packages/devel/bioc/html/regionReport.html always has a warning in the Windows build machine due to a mismatch in the version of Rtools installed. This is a bug in devtools and may have already been fixed (but not yet propagated to CRAN). IMO this should be reflected in the build shield. Dan I do like these changes and the addition of shields =) On Thu, May 14, 2015 at 10:56 AM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Jim Hester james.f.hes...@gmail.com To: Martin Morgan mtmor...@fredhutch.org Cc: bioc-devel@r-project.org Sent: Thursday, May 14, 2015 7:53:03 AM Subject: Re: [Bioc-devel] Use and Usability metrics / shields The common shield convention is to use blue or orange when the information is not qualitatively good or bad, but the color choice is just subjective in the end. It does seem though that we should indicate the non-changing nature of these shields with some kind of color change. Perhaps we can come up with one that works with the other design elements on the page. BTW, the 'posts' tag does change color; if there are 0 posts tagged with a package name, the shield is yellow; otherwise it's green. Dan On Thu, May 14, 2015 at 10:47 AM, Martin Morgan mtmor...@fredhutch.org wrote: On 05/10/2015 11:39 AM, COMMO Frederic wrote: Dear Martin, All of these suggestions sound good. Wolfgang's suggestion regarding possible associated papers might be also great. Another useful information would be to point to other publications where a given package was used, and cited. I don't know if it's technically possible, but it would be greatly informative to know how frequently
Re: [Bioc-devel] Use and Usability metrics / shields
- Original Message - From: Leonardo Collado Torres lcoll...@jhu.edu To: Dan Tenenbaum dtene...@fredhutch.org Cc: bioc-devel@r-project.org Sent: Friday, June 12, 2015 11:43:09 AM Subject: Re: [Bioc-devel] Use and Usability metrics / shields Awesome! Here's the code in case others want to add the shields to their github readme files. https://gist.github.com/lcolladotor/de2e0b67fbf33518b922 derfinder example (software package) https://github.com/lcolladotor/derfinder derfinderData example (experiment data package) https://github.com/leekgroup/derfinderData Cool! Note that some shields will be the same for release and devel; others will differ, such as the platforms shield. So since your repos is presumably mapped to the devel version of your package, you should pull the 'platforms' shield from 'shields/availability/devel' instead of 'shields/availability/release'. Dan On Fri, Jun 12, 2015 at 12:32 AM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Leonardo Collado Torres lcoll...@jhu.edu To: Dan Tenenbaum dtene...@fredhutch.org Cc: bioc-devel@r-project.org Sent: Thursday, June 11, 2015 9:26:13 PM Subject: Re: [Bioc-devel] Use and Usability metrics / shields Is it ok if we use the Bioconductor shields elsewhere? For example, in a github repo landing page or in our website listing the software we've contributed to. In particular, I'm thinking of adding http://www.bioconductor.org/shields/posts/derfinder.svg (and the other shields) to https://github.com/lcolladotor/derfinder to go along the Travis CI shield I use right now. Feel free, that was part of the idea. Dan On Thu, Jun 4, 2015 at 11:22 AM, Jim Hester james.f.hes...@gmail.com wrote: Henrik, While I proposed the idea for the shields/badges Dan gets all the credit for the implementation. As far as your (implied) idea of a coverage badge, the thought had occurred to us! Jim On Wed, May 20, 2015 at 1:34 PM, Henrik Bengtsson henrik.bengts...@ucsf.edu wrote: So, lots of things are happening in a few months: Jim Hester starts working at Bioconductor, we get Bioc shields/badges, Jim's covr package is released on CRAN, snare drum, ... am I to eager if I already now start wishing for a hi-hat as well? /Henrik On Tue, May 19, 2015 at 12:47 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Leonardo Collado Torres lcoll...@jhu.edu To: Dan Tenenbaum dtene...@fredhutch.org Cc: Jim Hester james.f.hes...@gmail.com, bioc-devel@r-project.org Sent: Tuesday, May 19, 2015 12:37:18 PM Subject: Re: [Bioc-devel] Use and Usability metrics / shields Regarding the 'posts' tag, I can see that it includes a closed questions component. For example, http://www.bioconductor.org/packages/release/bioc/html/derfinder.html is 3/1/9/0 right now meaning that 0 questions are closed. From https://support.bioconductor.org/info/faq/, only moderators can close questions. That seems like quite a bit of work for the moderators. So maybe it would be best to drop the closed questions component. Or alternatively, can the author of a package moderate the posts that have a tag corresponding to their package? Perhaps the wording is wrong; what 'closed' is supposed to mean is that the original poster has accepted an answer. I'll change 'closed' to 'accepted'. As for 'build: warnings', it seems like it will show for some devel packages all the time. For example, http://www.bioconductor.org/packages/devel/bioc/html/regionReport.html always has a warning in the Windows build machine due to a mismatch in the version of Rtools installed. This is a bug in devtools and may have already been fixed (but not yet propagated to CRAN). IMO this should be reflected in the build shield. Dan I do like these changes and the addition of shields =) On Thu, May 14, 2015 at 10:56 AM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Jim Hester james.f.hes...@gmail.com To: Martin Morgan mtmor...@fredhutch.org Cc: bioc-devel@r-project.org Sent: Thursday, May 14, 2015 7:53:03 AM Subject: Re: [Bioc-devel] Use and Usability metrics / shields The common shield convention is to use blue or orange when the information is not qualitatively good or bad, but the color choice is just subjective in the end. It does seem though that we should indicate the non-changing nature of these shields with some kind of color change. Perhaps we can come up with one that works with the other
Re: [Bioc-devel] Use and Usability metrics / shields
Ahh, I missed the 2 versions on the platforms shield. I am using both build shields. I'll make some edits then. On Fri, Jun 12, 2015 at 2:49 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Leonardo Collado Torres lcoll...@jhu.edu To: Dan Tenenbaum dtene...@fredhutch.org Cc: bioc-devel@r-project.org Sent: Friday, June 12, 2015 11:43:09 AM Subject: Re: [Bioc-devel] Use and Usability metrics / shields Awesome! Here's the code in case others want to add the shields to their github readme files. https://gist.github.com/lcolladotor/de2e0b67fbf33518b922 derfinder example (software package) https://github.com/lcolladotor/derfinder derfinderData example (experiment data package) https://github.com/leekgroup/derfinderData Cool! Note that some shields will be the same for release and devel; others will differ, such as the platforms shield. So since your repos is presumably mapped to the devel version of your package, you should pull the 'platforms' shield from 'shields/availability/devel' instead of 'shields/availability/release'. Dan On Fri, Jun 12, 2015 at 12:32 AM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Leonardo Collado Torres lcoll...@jhu.edu To: Dan Tenenbaum dtene...@fredhutch.org Cc: bioc-devel@r-project.org Sent: Thursday, June 11, 2015 9:26:13 PM Subject: Re: [Bioc-devel] Use and Usability metrics / shields Is it ok if we use the Bioconductor shields elsewhere? For example, in a github repo landing page or in our website listing the software we've contributed to. In particular, I'm thinking of adding http://www.bioconductor.org/shields/posts/derfinder.svg (and the other shields) to https://github.com/lcolladotor/derfinder to go along the Travis CI shield I use right now. Feel free, that was part of the idea. Dan On Thu, Jun 4, 2015 at 11:22 AM, Jim Hester james.f.hes...@gmail.com wrote: Henrik, While I proposed the idea for the shields/badges Dan gets all the credit for the implementation. As far as your (implied) idea of a coverage badge, the thought had occurred to us! Jim On Wed, May 20, 2015 at 1:34 PM, Henrik Bengtsson henrik.bengts...@ucsf.edu wrote: So, lots of things are happening in a few months: Jim Hester starts working at Bioconductor, we get Bioc shields/badges, Jim's covr package is released on CRAN, snare drum, ... am I to eager if I already now start wishing for a hi-hat as well? /Henrik On Tue, May 19, 2015 at 12:47 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Leonardo Collado Torres lcoll...@jhu.edu To: Dan Tenenbaum dtene...@fredhutch.org Cc: Jim Hester james.f.hes...@gmail.com, bioc-devel@r-project.org Sent: Tuesday, May 19, 2015 12:37:18 PM Subject: Re: [Bioc-devel] Use and Usability metrics / shields Regarding the 'posts' tag, I can see that it includes a closed questions component. For example, http://www.bioconductor.org/packages/release/bioc/html/derfinder.html is 3/1/9/0 right now meaning that 0 questions are closed. From https://support.bioconductor.org/info/faq/, only moderators can close questions. That seems like quite a bit of work for the moderators. So maybe it would be best to drop the closed questions component. Or alternatively, can the author of a package moderate the posts that have a tag corresponding to their package? Perhaps the wording is wrong; what 'closed' is supposed to mean is that the original poster has accepted an answer. I'll change 'closed' to 'accepted'. As for 'build: warnings', it seems like it will show for some devel packages all the time. For example, http://www.bioconductor.org/packages/devel/bioc/html/regionReport.html always has a warning in the Windows build machine due to a mismatch in the version of Rtools installed. This is a bug in devtools and may have already been fixed (but not yet propagated to CRAN). IMO this should be reflected in the build shield. Dan I do like these changes and the addition of shields =) On Thu, May 14, 2015 at 10:56 AM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Jim Hester james.f.hes...@gmail.com To: Martin Morgan mtmor...@fredhutch.org Cc: bioc-devel@r-project.org Sent: Thursday, May 14, 2015 7:53:03 AM Subject: Re: [Bioc-devel] Use and Usability metrics / shields The common shield convention is to use blue or orange when the information is not qualitatively good or bad, but the color choice is just subjective in the end. It does seem
Re: [Bioc-devel] Use and Usability metrics / shields
Is it ok if we use the Bioconductor shields elsewhere? For example, in a github repo landing page or in our website listing the software we've contributed to. In particular, I'm thinking of adding http://www.bioconductor.org/shields/posts/derfinder.svg (and the other shields) to https://github.com/lcolladotor/derfinder to go along the Travis CI shield I use right now. On Thu, Jun 4, 2015 at 11:22 AM, Jim Hester james.f.hes...@gmail.com wrote: Henrik, While I proposed the idea for the shields/badges Dan gets all the credit for the implementation. As far as your (implied) idea of a coverage badge, the thought had occurred to us! Jim On Wed, May 20, 2015 at 1:34 PM, Henrik Bengtsson henrik.bengts...@ucsf.edu wrote: So, lots of things are happening in a few months: Jim Hester starts working at Bioconductor, we get Bioc shields/badges, Jim's covr package is released on CRAN, snare drum, ... am I to eager if I already now start wishing for a hi-hat as well? /Henrik On Tue, May 19, 2015 at 12:47 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Leonardo Collado Torres lcoll...@jhu.edu To: Dan Tenenbaum dtene...@fredhutch.org Cc: Jim Hester james.f.hes...@gmail.com, bioc-devel@r-project.org Sent: Tuesday, May 19, 2015 12:37:18 PM Subject: Re: [Bioc-devel] Use and Usability metrics / shields Regarding the 'posts' tag, I can see that it includes a closed questions component. For example, http://www.bioconductor.org/packages/release/bioc/html/derfinder.html is 3/1/9/0 right now meaning that 0 questions are closed. From https://support.bioconductor.org/info/faq/, only moderators can close questions. That seems like quite a bit of work for the moderators. So maybe it would be best to drop the closed questions component. Or alternatively, can the author of a package moderate the posts that have a tag corresponding to their package? Perhaps the wording is wrong; what 'closed' is supposed to mean is that the original poster has accepted an answer. I'll change 'closed' to 'accepted'. As for 'build: warnings', it seems like it will show for some devel packages all the time. For example, http://www.bioconductor.org/packages/devel/bioc/html/regionReport.html always has a warning in the Windows build machine due to a mismatch in the version of Rtools installed. This is a bug in devtools and may have already been fixed (but not yet propagated to CRAN). IMO this should be reflected in the build shield. Dan I do like these changes and the addition of shields =) On Thu, May 14, 2015 at 10:56 AM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Jim Hester james.f.hes...@gmail.com To: Martin Morgan mtmor...@fredhutch.org Cc: bioc-devel@r-project.org Sent: Thursday, May 14, 2015 7:53:03 AM Subject: Re: [Bioc-devel] Use and Usability metrics / shields The common shield convention is to use blue or orange when the information is not qualitatively good or bad, but the color choice is just subjective in the end. It does seem though that we should indicate the non-changing nature of these shields with some kind of color change. Perhaps we can come up with one that works with the other design elements on the page. BTW, the 'posts' tag does change color; if there are 0 posts tagged with a package name, the shield is yellow; otherwise it's green. Dan On Thu, May 14, 2015 at 10:47 AM, Martin Morgan mtmor...@fredhutch.org wrote: On 05/10/2015 11:39 AM, COMMO Frederic wrote: Dear Martin, All of these suggestions sound good. Wolfgang's suggestion regarding possible associated papers might be also great. Another useful information would be to point to other publications where a given package was used, and cited. I don't know if it's technically possible, but it would be greatly informative to know how frequently a package is used, and how it performs, in real contexts. Frederic Commo Bioinformatics, U981 Gustave Roussy De : Bioc-devel [bioc-devel-boun...@r-project.org] de la part de Wolfgang Huber [whu...@embl.de] Date d'envoi : samedi 9 mai 2015 19:57 À : Martin Morgan Cc: bioc-devel@r-project.org Objet : Re: [Bioc-devel] Use and Usability metrics / shields Dear Martin great idea. Current build status” could perhaps be wrapped with Cross-platform availability” into some sort of “Availability / Accessibility”? I wonder how informative it would be to make metrics such as (i) citations of the associated paper (ii) full-text mentions e.g. in PubmedCentral actually useful. (i) could be flawed if package and paper are diverged; (ii) would require good
Re: [Bioc-devel] Use and Usability metrics / shields
- Original Message - From: Leonardo Collado Torres lcoll...@jhu.edu To: Dan Tenenbaum dtene...@fredhutch.org Cc: bioc-devel@r-project.org Sent: Thursday, June 11, 2015 9:26:13 PM Subject: Re: [Bioc-devel] Use and Usability metrics / shields Is it ok if we use the Bioconductor shields elsewhere? For example, in a github repo landing page or in our website listing the software we've contributed to. In particular, I'm thinking of adding http://www.bioconductor.org/shields/posts/derfinder.svg (and the other shields) to https://github.com/lcolladotor/derfinder to go along the Travis CI shield I use right now. Feel free, that was part of the idea. Dan On Thu, Jun 4, 2015 at 11:22 AM, Jim Hester james.f.hes...@gmail.com wrote: Henrik, While I proposed the idea for the shields/badges Dan gets all the credit for the implementation. As far as your (implied) idea of a coverage badge, the thought had occurred to us! Jim On Wed, May 20, 2015 at 1:34 PM, Henrik Bengtsson henrik.bengts...@ucsf.edu wrote: So, lots of things are happening in a few months: Jim Hester starts working at Bioconductor, we get Bioc shields/badges, Jim's covr package is released on CRAN, snare drum, ... am I to eager if I already now start wishing for a hi-hat as well? /Henrik On Tue, May 19, 2015 at 12:47 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Leonardo Collado Torres lcoll...@jhu.edu To: Dan Tenenbaum dtene...@fredhutch.org Cc: Jim Hester james.f.hes...@gmail.com, bioc-devel@r-project.org Sent: Tuesday, May 19, 2015 12:37:18 PM Subject: Re: [Bioc-devel] Use and Usability metrics / shields Regarding the 'posts' tag, I can see that it includes a closed questions component. For example, http://www.bioconductor.org/packages/release/bioc/html/derfinder.html is 3/1/9/0 right now meaning that 0 questions are closed. From https://support.bioconductor.org/info/faq/, only moderators can close questions. That seems like quite a bit of work for the moderators. So maybe it would be best to drop the closed questions component. Or alternatively, can the author of a package moderate the posts that have a tag corresponding to their package? Perhaps the wording is wrong; what 'closed' is supposed to mean is that the original poster has accepted an answer. I'll change 'closed' to 'accepted'. As for 'build: warnings', it seems like it will show for some devel packages all the time. For example, http://www.bioconductor.org/packages/devel/bioc/html/regionReport.html always has a warning in the Windows build machine due to a mismatch in the version of Rtools installed. This is a bug in devtools and may have already been fixed (but not yet propagated to CRAN). IMO this should be reflected in the build shield. Dan I do like these changes and the addition of shields =) On Thu, May 14, 2015 at 10:56 AM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Jim Hester james.f.hes...@gmail.com To: Martin Morgan mtmor...@fredhutch.org Cc: bioc-devel@r-project.org Sent: Thursday, May 14, 2015 7:53:03 AM Subject: Re: [Bioc-devel] Use and Usability metrics / shields The common shield convention is to use blue or orange when the information is not qualitatively good or bad, but the color choice is just subjective in the end. It does seem though that we should indicate the non-changing nature of these shields with some kind of color change. Perhaps we can come up with one that works with the other design elements on the page. BTW, the 'posts' tag does change color; if there are 0 posts tagged with a package name, the shield is yellow; otherwise it's green. Dan On Thu, May 14, 2015 at 10:47 AM, Martin Morgan mtmor...@fredhutch.org wrote: On 05/10/2015 11:39 AM, COMMO Frederic wrote: Dear Martin, All of these suggestions sound good. Wolfgang's suggestion regarding possible associated papers might be also great. Another useful information would be to point to other publications where a given package was used, and cited. I don't know if it's technically possible, but it would be greatly informative to know how frequently a package is used, and how it performs, in real contexts. Frederic Commo Bioinformatics, U981 Gustave Roussy De : Bioc-devel [bioc-devel-boun...@r-project.org] de la part de Wolfgang Huber [whu...@embl.de] Date d'envoi : samedi 9 mai 2015 19:57 À : Martin Morgan Cc: bioc-devel@r
Re: [Bioc-devel] Use and Usability metrics / shields
So, lots of things are happening in a few months: Jim Hester starts working at Bioconductor, we get Bioc shields/badges, Jim's covr package is released on CRAN, snare drum, ... am I to eager if I already now start wishing for a hi-hat as well? /Henrik On Tue, May 19, 2015 at 12:47 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Leonardo Collado Torres lcoll...@jhu.edu To: Dan Tenenbaum dtene...@fredhutch.org Cc: Jim Hester james.f.hes...@gmail.com, bioc-devel@r-project.org Sent: Tuesday, May 19, 2015 12:37:18 PM Subject: Re: [Bioc-devel] Use and Usability metrics / shields Regarding the 'posts' tag, I can see that it includes a closed questions component. For example, http://www.bioconductor.org/packages/release/bioc/html/derfinder.html is 3/1/9/0 right now meaning that 0 questions are closed. From https://support.bioconductor.org/info/faq/, only moderators can close questions. That seems like quite a bit of work for the moderators. So maybe it would be best to drop the closed questions component. Or alternatively, can the author of a package moderate the posts that have a tag corresponding to their package? Perhaps the wording is wrong; what 'closed' is supposed to mean is that the original poster has accepted an answer. I'll change 'closed' to 'accepted'. As for 'build: warnings', it seems like it will show for some devel packages all the time. For example, http://www.bioconductor.org/packages/devel/bioc/html/regionReport.html always has a warning in the Windows build machine due to a mismatch in the version of Rtools installed. This is a bug in devtools and may have already been fixed (but not yet propagated to CRAN). IMO this should be reflected in the build shield. Dan I do like these changes and the addition of shields =) On Thu, May 14, 2015 at 10:56 AM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Jim Hester james.f.hes...@gmail.com To: Martin Morgan mtmor...@fredhutch.org Cc: bioc-devel@r-project.org Sent: Thursday, May 14, 2015 7:53:03 AM Subject: Re: [Bioc-devel] Use and Usability metrics / shields The common shield convention is to use blue or orange when the information is not qualitatively good or bad, but the color choice is just subjective in the end. It does seem though that we should indicate the non-changing nature of these shields with some kind of color change. Perhaps we can come up with one that works with the other design elements on the page. BTW, the 'posts' tag does change color; if there are 0 posts tagged with a package name, the shield is yellow; otherwise it's green. Dan On Thu, May 14, 2015 at 10:47 AM, Martin Morgan mtmor...@fredhutch.org wrote: On 05/10/2015 11:39 AM, COMMO Frederic wrote: Dear Martin, All of these suggestions sound good. Wolfgang's suggestion regarding possible associated papers might be also great. Another useful information would be to point to other publications where a given package was used, and cited. I don't know if it's technically possible, but it would be greatly informative to know how frequently a package is used, and how it performs, in real contexts. Frederic Commo Bioinformatics, U981 Gustave Roussy De : Bioc-devel [bioc-devel-boun...@r-project.org] de la part de Wolfgang Huber [whu...@embl.de] Date d'envoi : samedi 9 mai 2015 19:57 À : Martin Morgan Cc: bioc-devel@r-project.org Objet : Re: [Bioc-devel] Use and Usability metrics / shields Dear Martin great idea. Current build status” could perhaps be wrapped with Cross-platform availability” into some sort of “Availability / Accessibility”? I wonder how informative it would be to make metrics such as (i) citations of the associated paper (ii) full-text mentions e.g. in PubmedCentral actually useful. (i) could be flawed if package and paper are diverged; (ii) would require good disambiguation, e.g. like bioNerDS http://www.biomedcentral.com/1471-2105/14/194 (or other tools? not my expertise). Do we have someone with capabilities in this area on this list? Thanks for these suggestions. I like the idea of linking into the scientific literature, initially as part of the 'Citation' section on each landing page rather than as a shield (maybe a shield in the long term). As Wolfgang mentions it is a little more challenging than a one-liner to match the information available from a CITATION file (or automatically generated) to an appropriate search in PubMed, and because citations are an important formal metric it seems important to get this more-or-less right. For what it's worth the more-or-less continuous stream of papers citing 'Biocondcutor' are listed
Re: [Bioc-devel] Use and Usability metrics / shields
- Original Message - From: Leonardo Collado Torres lcoll...@jhu.edu To: Dan Tenenbaum dtene...@fredhutch.org Cc: Jim Hester james.f.hes...@gmail.com, bioc-devel@r-project.org Sent: Tuesday, May 19, 2015 12:37:18 PM Subject: Re: [Bioc-devel] Use and Usability metrics / shields Regarding the 'posts' tag, I can see that it includes a closed questions component. For example, http://www.bioconductor.org/packages/release/bioc/html/derfinder.html is 3/1/9/0 right now meaning that 0 questions are closed. From https://support.bioconductor.org/info/faq/, only moderators can close questions. That seems like quite a bit of work for the moderators. So maybe it would be best to drop the closed questions component. Or alternatively, can the author of a package moderate the posts that have a tag corresponding to their package? Perhaps the wording is wrong; what 'closed' is supposed to mean is that the original poster has accepted an answer. I'll change 'closed' to 'accepted'. As for 'build: warnings', it seems like it will show for some devel packages all the time. For example, http://www.bioconductor.org/packages/devel/bioc/html/regionReport.html always has a warning in the Windows build machine due to a mismatch in the version of Rtools installed. This is a bug in devtools and may have already been fixed (but not yet propagated to CRAN). IMO this should be reflected in the build shield. Dan I do like these changes and the addition of shields =) On Thu, May 14, 2015 at 10:56 AM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Jim Hester james.f.hes...@gmail.com To: Martin Morgan mtmor...@fredhutch.org Cc: bioc-devel@r-project.org Sent: Thursday, May 14, 2015 7:53:03 AM Subject: Re: [Bioc-devel] Use and Usability metrics / shields The common shield convention is to use blue or orange when the information is not qualitatively good or bad, but the color choice is just subjective in the end. It does seem though that we should indicate the non-changing nature of these shields with some kind of color change. Perhaps we can come up with one that works with the other design elements on the page. BTW, the 'posts' tag does change color; if there are 0 posts tagged with a package name, the shield is yellow; otherwise it's green. Dan On Thu, May 14, 2015 at 10:47 AM, Martin Morgan mtmor...@fredhutch.org wrote: On 05/10/2015 11:39 AM, COMMO Frederic wrote: Dear Martin, All of these suggestions sound good. Wolfgang's suggestion regarding possible associated papers might be also great. Another useful information would be to point to other publications where a given package was used, and cited. I don't know if it's technically possible, but it would be greatly informative to know how frequently a package is used, and how it performs, in real contexts. Frederic Commo Bioinformatics, U981 Gustave Roussy De : Bioc-devel [bioc-devel-boun...@r-project.org] de la part de Wolfgang Huber [whu...@embl.de] Date d'envoi : samedi 9 mai 2015 19:57 À : Martin Morgan Cc: bioc-devel@r-project.org Objet : Re: [Bioc-devel] Use and Usability metrics / shields Dear Martin great idea. Current build status” could perhaps be wrapped with Cross-platform availability” into some sort of “Availability / Accessibility”? I wonder how informative it would be to make metrics such as (i) citations of the associated paper (ii) full-text mentions e.g. in PubmedCentral actually useful. (i) could be flawed if package and paper are diverged; (ii) would require good disambiguation, e.g. like bioNerDS http://www.biomedcentral.com/1471-2105/14/194 (or other tools? not my expertise). Do we have someone with capabilities in this area on this list? Thanks for these suggestions. I like the idea of linking into the scientific literature, initially as part of the 'Citation' section on each landing page rather than as a shield (maybe a shield in the long term). As Wolfgang mentions it is a little more challenging than a one-liner to match the information available from a CITATION file (or automatically generated) to an appropriate search in PubMed, and because citations are an important formal metric it seems important to get this more-or-less right. For what it's worth the more-or-less continuous stream of papers citing 'Biocondcutor' are listed at http://bioconductor.org/help/publications/ The links in the 'Literature Search' box query various resources for use of the term 'Bioconductor'. We have so far kept the distinction between 'available' and 'build', partly because builds sometimes fail for transient (e.g., connectivity) reasons
Re: [Bioc-devel] Use and Usability metrics / shields
Regarding the 'posts' tag, I can see that it includes a closed questions component. For example, http://www.bioconductor.org/packages/release/bioc/html/derfinder.html is 3/1/9/0 right now meaning that 0 questions are closed. From https://support.bioconductor.org/info/faq/, only moderators can close questions. That seems like quite a bit of work for the moderators. So maybe it would be best to drop the closed questions component. Or alternatively, can the author of a package moderate the posts that have a tag corresponding to their package? As for 'build: warnings', it seems like it will show for some devel packages all the time. For example, http://www.bioconductor.org/packages/devel/bioc/html/regionReport.html always has a warning in the Windows build machine due to a mismatch in the version of Rtools installed. I do like these changes and the addition of shields =) On Thu, May 14, 2015 at 10:56 AM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Jim Hester james.f.hes...@gmail.com To: Martin Morgan mtmor...@fredhutch.org Cc: bioc-devel@r-project.org Sent: Thursday, May 14, 2015 7:53:03 AM Subject: Re: [Bioc-devel] Use and Usability metrics / shields The common shield convention is to use blue or orange when the information is not qualitatively good or bad, but the color choice is just subjective in the end. It does seem though that we should indicate the non-changing nature of these shields with some kind of color change. Perhaps we can come up with one that works with the other design elements on the page. BTW, the 'posts' tag does change color; if there are 0 posts tagged with a package name, the shield is yellow; otherwise it's green. Dan On Thu, May 14, 2015 at 10:47 AM, Martin Morgan mtmor...@fredhutch.org wrote: On 05/10/2015 11:39 AM, COMMO Frederic wrote: Dear Martin, All of these suggestions sound good. Wolfgang's suggestion regarding possible associated papers might be also great. Another useful information would be to point to other publications where a given package was used, and cited. I don't know if it's technically possible, but it would be greatly informative to know how frequently a package is used, and how it performs, in real contexts. Frederic Commo Bioinformatics, U981 Gustave Roussy De : Bioc-devel [bioc-devel-boun...@r-project.org] de la part de Wolfgang Huber [whu...@embl.de] Date d'envoi : samedi 9 mai 2015 19:57 À : Martin Morgan Cc: bioc-devel@r-project.org Objet : Re: [Bioc-devel] Use and Usability metrics / shields Dear Martin great idea. Current build status” could perhaps be wrapped with Cross-platform availability” into some sort of “Availability / Accessibility”? I wonder how informative it would be to make metrics such as (i) citations of the associated paper (ii) full-text mentions e.g. in PubmedCentral actually useful. (i) could be flawed if package and paper are diverged; (ii) would require good disambiguation, e.g. like bioNerDS http://www.biomedcentral.com/1471-2105/14/194 (or other tools? not my expertise). Do we have someone with capabilities in this area on this list? Thanks for these suggestions. I like the idea of linking into the scientific literature, initially as part of the 'Citation' section on each landing page rather than as a shield (maybe a shield in the long term). As Wolfgang mentions it is a little more challenging than a one-liner to match the information available from a CITATION file (or automatically generated) to an appropriate search in PubMed, and because citations are an important formal metric it seems important to get this more-or-less right. For what it's worth the more-or-less continuous stream of papers citing 'Biocondcutor' are listed at http://bioconductor.org/help/publications/ The links in the 'Literature Search' box query various resources for use of the term 'Bioconductor'. We have so far kept the distinction between 'available' and 'build', partly because builds sometimes fail for transient (e.g., connectivity) reasons or, in devel, because of an incomplete check-in that does not compromise the end-user availability and functionality of the version available via biocLite(). It's kind of amusing that (a) most of the information was already available, often on the landing page (like the links to build reports that Henrik mentions, or years in bioc), so the shields are serving just to emphasize these; and (b) the 'green' implies some-how 'good', but many of the shields (e.g., years in Bioc, posts, commits, downloads) are actually never not green. Maybe these shields should be white? Thanks again for the feedback; initial response seems to be positive. Martin PS Martin you’ll like Fig. 2 of their paper. Wolfgang
Re: [Bioc-devel] Use and Usability metrics / shields
- Original Message - From: Wolfgang Huber whu...@embl.de To: Dan Tenenbaum dtene...@fredhutch.org Cc: bioc-devel@r-project.org Sent: Thursday, May 14, 2015 4:03:54 AM Subject: Re: [Bioc-devel] Use and Usability metrics / shields Can it be that the “in Bioc” shield is incorrect? For instance, it says “9.98 years” for vsn but the first commit was in Oct 2002 Curiously “9.98 years” is stated for many old packages - surely we can use R for more precise date arithmetic? It is not counting from the first commit (as it says in the tooltip text) but from the day of the first release in which the package appeared. So it does not count the time that the package is in devel only. Dan Cheers Wolfgang On May 13, 2015, at 21:36 GMT+2, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Henrik Bengtsson henrik.bengts...@ucsf.edu To: COMMO Frederic frederic.co...@gustaveroussy.fr Cc: bioc-devel@r-project.org Sent: Wednesday, May 13, 2015 12:28:54 PM Subject: Re: [Bioc-devel] Use and Usability metrics / shields Sweet; you went live with the badges/shields, e.g. http://bioconductor.org/packages/release/bioc/html/affxparser.html A positive side effect is that now there's a link from the package page to to the package's check results, which I always wanted :) That was there before (and still is, see the bottom of the Details section). But yes, it was not very visible. Dan Thanks for adding this /Henrik On Sun, May 10, 2015 at 11:39 AM, COMMO Frederic frederic.co...@gustaveroussy.fr wrote: Dear Martin, All of these suggestions sound good. Wolfgang's suggestion regarding possible associated papers might be also great. Another useful information would be to point to other publications where a given package was used, and cited. I don't know if it's technically possible, but it would be greatly informative to know how frequently a package is used, and how it performs, in real contexts. Frederic Commo Bioinformatics, U981 Gustave Roussy De : Bioc-devel [bioc-devel-boun...@r-project.org] de la part de Wolfgang Huber [whu...@embl.de] Date d'envoi : samedi 9 mai 2015 19:57 À : Martin Morgan Cc: bioc-devel@r-project.org Objet : Re: [Bioc-devel] Use and Usability metrics / shields Dear Martin great idea. Current build status” could perhaps be wrapped with Cross-platform availability” into some sort of “Availability / Accessibility”? I wonder how informative it would be to make metrics such as (i) citations of the associated paper (ii) full-text mentions e.g. in PubmedCentral actually useful. (i) could be flawed if package and paper are diverged; (ii) would require good disambiguation, e.g. like bioNerDS http://www.biomedcentral.com/1471-2105/14/194 (or other tools? not my expertise). Do we have someone with capabilities in this area on this list? PS Martin you’ll like Fig. 2 of their paper. Wolfgang On May 9, 2015, at 19:15 GMT+2, Martin Morgan mtmor...@fredhutch.org wrote: Bioc developers! It's important that our users be able to identify packages that are suitable for their research question. Obviously a first step is to identify packages in the appropriate research domain, for instance through biocViews. http://bioconductor.org/packages/release/ We'd like to help users further prioritize their efforts by summarizing use and usability. Metrics include: - Cross-platform availability -- biocLite()-able from all or only some platforms - Support forum activity -- questions and comments / responses, 6 month window - Download percentile -- top 5, 20, 50%, or 'available' - Current build status -- errors or warnings on some or all platforms - Developer activity -- commits in the last 6 months - Historical presence -- years in Bioconductor Obviously the metrics are imperfect, so constructive feedback welcome -- we think the above capture in a more-or-less objective and computable way the major axes influencing use and usability. We initially intend to prominently display 'shields' (small graphical icons) on package landing pages. Thanks in advance for your comments, Martin Morgan Bioconductor -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org
Re: [Bioc-devel] Use and Usability metrics / shields
The common shield convention is to use blue or orange when the information is not qualitatively good or bad, but the color choice is just subjective in the end. On Thu, May 14, 2015 at 10:47 AM, Martin Morgan mtmor...@fredhutch.org wrote: On 05/10/2015 11:39 AM, COMMO Frederic wrote: Dear Martin, All of these suggestions sound good. Wolfgang's suggestion regarding possible associated papers might be also great. Another useful information would be to point to other publications where a given package was used, and cited. I don't know if it's technically possible, but it would be greatly informative to know how frequently a package is used, and how it performs, in real contexts. Frederic Commo Bioinformatics, U981 Gustave Roussy De : Bioc-devel [bioc-devel-boun...@r-project.org] de la part de Wolfgang Huber [whu...@embl.de] Date d'envoi : samedi 9 mai 2015 19:57 À : Martin Morgan Cc: bioc-devel@r-project.org Objet : Re: [Bioc-devel] Use and Usability metrics / shields Dear Martin great idea. Current build status” could perhaps be wrapped with Cross-platform availability” into some sort of “Availability / Accessibility”? I wonder how informative it would be to make metrics such as (i) citations of the associated paper (ii) full-text mentions e.g. in PubmedCentral actually useful. (i) could be flawed if package and paper are diverged; (ii) would require good disambiguation, e.g. like bioNerDS http://www.biomedcentral.com/1471-2105/14/194 (or other tools? not my expertise). Do we have someone with capabilities in this area on this list? Thanks for these suggestions. I like the idea of linking into the scientific literature, initially as part of the 'Citation' section on each landing page rather than as a shield (maybe a shield in the long term). As Wolfgang mentions it is a little more challenging than a one-liner to match the information available from a CITATION file (or automatically generated) to an appropriate search in PubMed, and because citations are an important formal metric it seems important to get this more-or-less right. For what it's worth the more-or-less continuous stream of papers citing 'Biocondcutor' are listed at http://bioconductor.org/help/publications/ The links in the 'Literature Search' box query various resources for use of the term 'Bioconductor'. We have so far kept the distinction between 'available' and 'build', partly because builds sometimes fail for transient (e.g., connectivity) reasons or, in devel, because of an incomplete check-in that does not compromise the end-user availability and functionality of the version available via biocLite(). It's kind of amusing that (a) most of the information was already available, often on the landing page (like the links to build reports that Henrik mentions, or years in bioc), so the shields are serving just to emphasize these; and (b) the 'green' implies some-how 'good', but many of the shields (e.g., years in Bioc, posts, commits, downloads) are actually never not green. Maybe these shields should be white? Thanks again for the feedback; initial response seems to be positive. Martin PS Martin you’ll like Fig. 2 of their paper. Wolfgang On May 9, 2015, at 19:15 GMT+2, Martin Morgan mtmor...@fredhutch.org wrote: Bioc developers! It's important that our users be able to identify packages that are suitable for their research question. Obviously a first step is to identify packages in the appropriate research domain, for instance through biocViews. http://bioconductor.org/packages/release/ We'd like to help users further prioritize their efforts by summarizing use and usability. Metrics include: - Cross-platform availability -- biocLite()-able from all or only some platforms - Support forum activity -- questions and comments / responses, 6 month window - Download percentile -- top 5, 20, 50%, or 'available' - Current build status -- errors or warnings on some or all platforms - Developer activity -- commits in the last 6 months - Historical presence -- years in Bioconductor Obviously the metrics are imperfect, so constructive feedback welcome -- we think the above capture in a more-or-less objective and computable way the major axes influencing use and usability. We initially intend to prominently display 'shields' (small graphical icons) on package landing pages. Thanks in advance for your comments, Martin Morgan Bioconductor -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc
Re: [Bioc-devel] Use and Usability metrics / shields
- Original Message - From: Jim Hester james.f.hes...@gmail.com To: Martin Morgan mtmor...@fredhutch.org Cc: bioc-devel@r-project.org Sent: Thursday, May 14, 2015 7:53:03 AM Subject: Re: [Bioc-devel] Use and Usability metrics / shields The common shield convention is to use blue or orange when the information is not qualitatively good or bad, but the color choice is just subjective in the end. It does seem though that we should indicate the non-changing nature of these shields with some kind of color change. Perhaps we can come up with one that works with the other design elements on the page. BTW, the 'posts' tag does change color; if there are 0 posts tagged with a package name, the shield is yellow; otherwise it's green. Dan On Thu, May 14, 2015 at 10:47 AM, Martin Morgan mtmor...@fredhutch.org wrote: On 05/10/2015 11:39 AM, COMMO Frederic wrote: Dear Martin, All of these suggestions sound good. Wolfgang's suggestion regarding possible associated papers might be also great. Another useful information would be to point to other publications where a given package was used, and cited. I don't know if it's technically possible, but it would be greatly informative to know how frequently a package is used, and how it performs, in real contexts. Frederic Commo Bioinformatics, U981 Gustave Roussy De : Bioc-devel [bioc-devel-boun...@r-project.org] de la part de Wolfgang Huber [whu...@embl.de] Date d'envoi : samedi 9 mai 2015 19:57 À : Martin Morgan Cc: bioc-devel@r-project.org Objet : Re: [Bioc-devel] Use and Usability metrics / shields Dear Martin great idea. Current build status” could perhaps be wrapped with Cross-platform availability” into some sort of “Availability / Accessibility”? I wonder how informative it would be to make metrics such as (i) citations of the associated paper (ii) full-text mentions e.g. in PubmedCentral actually useful. (i) could be flawed if package and paper are diverged; (ii) would require good disambiguation, e.g. like bioNerDS http://www.biomedcentral.com/1471-2105/14/194 (or other tools? not my expertise). Do we have someone with capabilities in this area on this list? Thanks for these suggestions. I like the idea of linking into the scientific literature, initially as part of the 'Citation' section on each landing page rather than as a shield (maybe a shield in the long term). As Wolfgang mentions it is a little more challenging than a one-liner to match the information available from a CITATION file (or automatically generated) to an appropriate search in PubMed, and because citations are an important formal metric it seems important to get this more-or-less right. For what it's worth the more-or-less continuous stream of papers citing 'Biocondcutor' are listed at http://bioconductor.org/help/publications/ The links in the 'Literature Search' box query various resources for use of the term 'Bioconductor'. We have so far kept the distinction between 'available' and 'build', partly because builds sometimes fail for transient (e.g., connectivity) reasons or, in devel, because of an incomplete check-in that does not compromise the end-user availability and functionality of the version available via biocLite(). It's kind of amusing that (a) most of the information was already available, often on the landing page (like the links to build reports that Henrik mentions, or years in bioc), so the shields are serving just to emphasize these; and (b) the 'green' implies some-how 'good', but many of the shields (e.g., years in Bioc, posts, commits, downloads) are actually never not green. Maybe these shields should be white? Thanks again for the feedback; initial response seems to be positive. Martin PS Martin you’ll like Fig. 2 of their paper. Wolfgang On May 9, 2015, at 19:15 GMT+2, Martin Morgan mtmor...@fredhutch.org wrote: Bioc developers! It's important that our users be able to identify packages that are suitable for their research question. Obviously a first step is to identify packages in the appropriate research domain, for instance through biocViews. http://bioconductor.org/packages/release/ We'd like to help users further prioritize their efforts by summarizing use and usability. Metrics include: - Cross-platform availability -- biocLite()-able from all or only some platforms - Support forum activity -- questions and comments / responses, 6 month window - Download percentile -- top 5, 20, 50%, or 'available' - Current build status -- errors or warnings on some or all platforms - Developer activity -- commits in the last 6 months - Historical presence -- years in Bioconductor Obviously the metrics are imperfect, so
Re: [Bioc-devel] Use and Usability metrics / shields
Can it be that the “in Bioc” shield is incorrect? For instance, it says “9.98 years” for vsn but the first commit was in Oct 2002 Curiously “9.98 years” is stated for many old packages - surely we can use R for more precise date arithmetic? Cheers Wolfgang On May 13, 2015, at 21:36 GMT+2, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Henrik Bengtsson henrik.bengts...@ucsf.edu To: COMMO Frederic frederic.co...@gustaveroussy.fr Cc: bioc-devel@r-project.org Sent: Wednesday, May 13, 2015 12:28:54 PM Subject: Re: [Bioc-devel] Use and Usability metrics / shields Sweet; you went live with the badges/shields, e.g. http://bioconductor.org/packages/release/bioc/html/affxparser.html A positive side effect is that now there's a link from the package page to to the package's check results, which I always wanted :) That was there before (and still is, see the bottom of the Details section). But yes, it was not very visible. Dan Thanks for adding this /Henrik On Sun, May 10, 2015 at 11:39 AM, COMMO Frederic frederic.co...@gustaveroussy.fr wrote: Dear Martin, All of these suggestions sound good. Wolfgang's suggestion regarding possible associated papers might be also great. Another useful information would be to point to other publications where a given package was used, and cited. I don't know if it's technically possible, but it would be greatly informative to know how frequently a package is used, and how it performs, in real contexts. Frederic Commo Bioinformatics, U981 Gustave Roussy De : Bioc-devel [bioc-devel-boun...@r-project.org] de la part de Wolfgang Huber [whu...@embl.de] Date d'envoi : samedi 9 mai 2015 19:57 À : Martin Morgan Cc: bioc-devel@r-project.org Objet : Re: [Bioc-devel] Use and Usability metrics / shields Dear Martin great idea. Current build status” could perhaps be wrapped with Cross-platform availability” into some sort of “Availability / Accessibility”? I wonder how informative it would be to make metrics such as (i) citations of the associated paper (ii) full-text mentions e.g. in PubmedCentral actually useful. (i) could be flawed if package and paper are diverged; (ii) would require good disambiguation, e.g. like bioNerDS http://www.biomedcentral.com/1471-2105/14/194 (or other tools? not my expertise). Do we have someone with capabilities in this area on this list? PS Martin you’ll like Fig. 2 of their paper. Wolfgang On May 9, 2015, at 19:15 GMT+2, Martin Morgan mtmor...@fredhutch.org wrote: Bioc developers! It's important that our users be able to identify packages that are suitable for their research question. Obviously a first step is to identify packages in the appropriate research domain, for instance through biocViews. http://bioconductor.org/packages/release/ We'd like to help users further prioritize their efforts by summarizing use and usability. Metrics include: - Cross-platform availability -- biocLite()-able from all or only some platforms - Support forum activity -- questions and comments / responses, 6 month window - Download percentile -- top 5, 20, 50%, or 'available' - Current build status -- errors or warnings on some or all platforms - Developer activity -- commits in the last 6 months - Historical presence -- years in Bioconductor Obviously the metrics are imperfect, so constructive feedback welcome -- we think the above capture in a more-or-less objective and computable way the major axes influencing use and usability. We initially intend to prominently display 'shields' (small graphical icons) on package landing pages. Thanks in advance for your comments, Martin Morgan Bioconductor -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Use and Usability metrics / shields
- Original Message - From: Martin Morgan mtmor...@fredhutch.org To: bioc-devel@r-project.org Sent: Saturday, May 9, 2015 10:15:13 AM Subject: [Bioc-devel] Use and Usability metrics / shields Bioc developers! It's important that our users be able to identify packages that are suitable for their research question. Obviously a first step is to identify packages in the appropriate research domain, for instance through biocViews. http://bioconductor.org/packages/release/ We'd like to help users further prioritize their efforts by summarizing use and usability. Metrics include: - Cross-platform availability -- biocLite()-able from all or only some platforms - Support forum activity -- questions and comments / responses, 6 month window - Download percentile -- top 5, 20, 50%, or 'available' - Current build status -- errors or warnings on some or all platforms - Developer activity -- commits in the last 6 months - Historical presence -- years in Bioconductor Obviously the metrics are imperfect, so constructive feedback welcome -- we think the above capture in a more-or-less objective and computable way the major axes influencing use and usability. We initially intend to prominently display 'shields' (small graphical icons) on package landing pages. This has now been implemented. You can see it at e.g. http://bioconductor.org/packages/release/bioc/html/BiocGenerics.html The shields are also available for use externally, for example if you want to display build status on a README in Github. Just pull in the image from: http://bioconductor.org/shields/build/release/bioc/BiocGenerics.svg Note that devel has a different build shield: http://bioconductor.org/shields/build/devel/bioc/BiocGenerics.svg Thanks, Dan ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Use and Usability metrics / shields
Sweet; you went live with the badges/shields, e.g. http://bioconductor.org/packages/release/bioc/html/affxparser.html A positive side effect is that now there's a link from the package page to to the package's check results, which I always wanted :) Thanks for adding this /Henrik On Sun, May 10, 2015 at 11:39 AM, COMMO Frederic frederic.co...@gustaveroussy.fr wrote: Dear Martin, All of these suggestions sound good. Wolfgang's suggestion regarding possible associated papers might be also great. Another useful information would be to point to other publications where a given package was used, and cited. I don't know if it's technically possible, but it would be greatly informative to know how frequently a package is used, and how it performs, in real contexts. Frederic Commo Bioinformatics, U981 Gustave Roussy De : Bioc-devel [bioc-devel-boun...@r-project.org] de la part de Wolfgang Huber [whu...@embl.de] Date d'envoi : samedi 9 mai 2015 19:57 À : Martin Morgan Cc: bioc-devel@r-project.org Objet : Re: [Bioc-devel] Use and Usability metrics / shields Dear Martin great idea. Current build status” could perhaps be wrapped with Cross-platform availability” into some sort of “Availability / Accessibility”? I wonder how informative it would be to make metrics such as (i) citations of the associated paper (ii) full-text mentions e.g. in PubmedCentral actually useful. (i) could be flawed if package and paper are diverged; (ii) would require good disambiguation, e.g. like bioNerDS http://www.biomedcentral.com/1471-2105/14/194 (or other tools? not my expertise). Do we have someone with capabilities in this area on this list? PS Martin you’ll like Fig. 2 of their paper. Wolfgang On May 9, 2015, at 19:15 GMT+2, Martin Morgan mtmor...@fredhutch.org wrote: Bioc developers! It's important that our users be able to identify packages that are suitable for their research question. Obviously a first step is to identify packages in the appropriate research domain, for instance through biocViews. http://bioconductor.org/packages/release/ We'd like to help users further prioritize their efforts by summarizing use and usability. Metrics include: - Cross-platform availability -- biocLite()-able from all or only some platforms - Support forum activity -- questions and comments / responses, 6 month window - Download percentile -- top 5, 20, 50%, or 'available' - Current build status -- errors or warnings on some or all platforms - Developer activity -- commits in the last 6 months - Historical presence -- years in Bioconductor Obviously the metrics are imperfect, so constructive feedback welcome -- we think the above capture in a more-or-less objective and computable way the major axes influencing use and usability. We initially intend to prominently display 'shields' (small graphical icons) on package landing pages. Thanks in advance for your comments, Martin Morgan Bioconductor -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Use and Usability metrics / shields
Dear Martin, All of these suggestions sound good. Wolfgang's suggestion regarding possible associated papers might be also great. Another useful information would be to point to other publications where a given package was used, and cited. I don't know if it's technically possible, but it would be greatly informative to know how frequently a package is used, and how it performs, in real contexts. Frederic Commo Bioinformatics, U981 Gustave Roussy De : Bioc-devel [bioc-devel-boun...@r-project.org] de la part de Wolfgang Huber [whu...@embl.de] Date d'envoi : samedi 9 mai 2015 19:57 À : Martin Morgan Cc: bioc-devel@r-project.org Objet : Re: [Bioc-devel] Use and Usability metrics / shields Dear Martin great idea. Current build status” could perhaps be wrapped with Cross-platform availability” into some sort of “Availability / Accessibility”? I wonder how informative it would be to make metrics such as (i) citations of the associated paper (ii) full-text mentions e.g. in PubmedCentral actually useful. (i) could be flawed if package and paper are diverged; (ii) would require good disambiguation, e.g. like bioNerDS http://www.biomedcentral.com/1471-2105/14/194 (or other tools? not my expertise). Do we have someone with capabilities in this area on this list? PS Martin you’ll like Fig. 2 of their paper. Wolfgang On May 9, 2015, at 19:15 GMT+2, Martin Morgan mtmor...@fredhutch.org wrote: Bioc developers! It's important that our users be able to identify packages that are suitable for their research question. Obviously a first step is to identify packages in the appropriate research domain, for instance through biocViews. http://bioconductor.org/packages/release/ We'd like to help users further prioritize their efforts by summarizing use and usability. Metrics include: - Cross-platform availability -- biocLite()-able from all or only some platforms - Support forum activity -- questions and comments / responses, 6 month window - Download percentile -- top 5, 20, 50%, or 'available' - Current build status -- errors or warnings on some or all platforms - Developer activity -- commits in the last 6 months - Historical presence -- years in Bioconductor Obviously the metrics are imperfect, so constructive feedback welcome -- we think the above capture in a more-or-less objective and computable way the major axes influencing use and usability. We initially intend to prominently display 'shields' (small graphical icons) on package landing pages. Thanks in advance for your comments, Martin Morgan Bioconductor -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Use and Usability metrics / shields
Dear Martin great idea. Current build status” could perhaps be wrapped with Cross-platform availability” into some sort of “Availability / Accessibility”? I wonder how informative it would be to make metrics such as (i) citations of the associated paper (ii) full-text mentions e.g. in PubmedCentral actually useful. (i) could be flawed if package and paper are diverged; (ii) would require good disambiguation, e.g. like bioNerDS http://www.biomedcentral.com/1471-2105/14/194 (or other tools? not my expertise). Do we have someone with capabilities in this area on this list? PS Martin you’ll like Fig. 2 of their paper. Wolfgang On May 9, 2015, at 19:15 GMT+2, Martin Morgan mtmor...@fredhutch.org wrote: Bioc developers! It's important that our users be able to identify packages that are suitable for their research question. Obviously a first step is to identify packages in the appropriate research domain, for instance through biocViews. http://bioconductor.org/packages/release/ We'd like to help users further prioritize their efforts by summarizing use and usability. Metrics include: - Cross-platform availability -- biocLite()-able from all or only some platforms - Support forum activity -- questions and comments / responses, 6 month window - Download percentile -- top 5, 20, 50%, or 'available' - Current build status -- errors or warnings on some or all platforms - Developer activity -- commits in the last 6 months - Historical presence -- years in Bioconductor Obviously the metrics are imperfect, so constructive feedback welcome -- we think the above capture in a more-or-less objective and computable way the major axes influencing use and usability. We initially intend to prominently display 'shields' (small graphical icons) on package landing pages. Thanks in advance for your comments, Martin Morgan Bioconductor -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
