Hello, Has anyone considered applying for grant funding to develop BioConductor as a teaching tool for statistical analysis of microarray expression data? Part of the proposal could include developing some very basic documentation aimed at making BioConductor more accessible to clinicians, biology graduate students, or some other student population a funding agency might want to target. Yours, Ann Loraine On Feb 27, 2004, at 1:00 PM, Vincent Carey 525-2265 wrote: >> friendly", and even "adequately documented" may be completely >> different >> from the rest of humanity! I immediately thought of certain BioC >> packages I've recently bashed my head over (and over and over). > > the developers are fairly responsive to questions > >> >> At the end of the essay ESR presents a checklist for telling whether >> your software suffers from problems similar to the ones he describes. >> For the benefit of any package developers/maintainers who may still be >> reading this, here's my version of that checklist as revised >> specifically for Bioconductor: >> >> 1. What does the package look like to a computer person who isn't a >> statistician or a statistician who isn't a computer person? What >> would be the most obvious thing someone unfamiliar with your >> package would try to use it for... and if they did, would they >> succeed after having done nothing more than read the manpage? > > we've taken care to develop a "vignette" protocol in addition > to man pages so that the user may get a holistic view of a software > component's roles. all bioc packages have vignettes. admittedly > these are not perfect but they help to illustrate and test > interoperability. > >> 2. Is there any dialogue in the Tcl widgets which is a dead end, >> without giving guidance on what the choices actually do? >> (although >> if you read ESR's essay you might conclude that there's no point >> to even having widgets, since a GUI does not automatically >> translate into user friendliness) > > some widgets are extremely useful. no essay would convince > me to eliminate them. there is clearly scope for improvement > with some of them. we have taken care to provide widgetbuilding > tools so that user/developers dissatisfied with the behavior > of a given widget can try to design one that is more effective. > >> 3. The requirement that end-users read documentation is NOT a sign >> of >> failure for a program such as R which mostly lacks a UI... >> but... >> * Is every argument, method, and slot of every non- private >> object documented in the manpage >> *for that object* (rather than referring to some other >> manpage which in turn refers to another manpage, ad >> nauseum)? > > that is the intention of the documentation validation protocol > of R CMD check. it can be subverted, and when it is, we try > to remedy it. > >> * Are the usage examples you give in the manpage simple, >> general, and comprehensible both to statisticians who >> aren't >> computer people and computer people who aren't >> statisticians? Hint: gratuitous use of functions that >> aren't >> from the package you're documenting reduces >> comprehensibility. > > perhaps not. perhaps you have a better example to contribute. > again the vignettes help to provide context. there is also > a browser for vignettes called vExplorer > >> * Does the documentation rely on references to hardcopy >> publications to explain crucial portions of the object's >> functionality instead of using external references as >> supplementary/background material? > > perhaps. we have limited resources for what we are doing and > sometimes a demand must be made on the user or reader to > obtain an explanatory resource. > >> * If there is a significant number of usage scenarios where >> the default argument values will be inappropriate, is the >> user warned? >> * Are the manpages in sync with the current package version? > > they should be, and there are mechanisms for verifying this. > >> 4. Do you ever find yourself using any phrase resembling "The >> syntax >> is just like it is for the S-Plus version"? > > no. > >> 5. Does your project welcome and respond to usability feedback from >> non-expert users? > > yes. > >> 6. Do error messages give enough information to be able to >> distinguish between malformed input/arguments, platform >> limitations (memory, drive space, access permissions), problems >> in >> R itself, and other ("other" presumably being the real bugs)? > > in many cases, yes. in other cases, no. provide resources > so that we can add programming effort to exceptionhandling > features and this situation will improve. > >> >> Thank you for your patience in reading this. I don't pretend to >> understand the technical complexity of your work, nor your motivations >> for doing it. However, if you do write open source software such as >> Bioconductor packages, it would be logical to at least assume that you >> want other people to use your software. Hopefully the above >> considerations will assist in making that happen. > > it is happening. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

You might want to consider using commercial software with lots of pretty buttons and colorful windows to click on and with lots of black boxes crunching all the numbers for you. I, however, prefer using R and BioConductor because I don't like buttons, windows, and black boxes as much. I like to know what is going on behind the scenes. I like being able to change parameters and functions if necessary. So, thank you, BioConductor developers, for your work! You're doing a great job! Best, Johannes Quoting Alex F. Bokov <yjih74b02@sneakemail.com>: So here goes, I am about to risk getting myself blacklisted by the very people I can least afford to be blacklisted by, and at the very start of my career no less. Why am I taking this risk? Because I love Bioconductor, it's the most useful thing currently installed on my PC, and I'm deeply grateful to the developer and user community for making such a wonderful tool. The following constructive criticism is how I hope to make it better. Here is an essay by Eric S. Raymond describing the difficulties he had configuring a software package on Linux. Obviously the last person you'd think of as "computer illiterate", "lazy", or "clueless". http://www.catb.org/~esr/writings/cups-horror.html Once you wade through the technical minutia of his specific software struggle, the main message appears to be that software is often written by individuals who are so knowledgeable in their particular field that their idea of "obvious", "self explanatory", "intuitive", "user friendly", and even "adequately documented" may be completely different from the rest of humanity! I immediately thought of certain BioC packages I've recently bashed my head over (and over and over). At the end of the essay ESR presents a checklist for telling whether your software suffers from problems similar to the ones he describes. For the benefit of any package developers/maintainers who may still be reading this, here's my version of that checklist as revised specifically for Bioconductor: 1. What does the package look like to a computer person who isn't a statistician or a statistician who isn't a computer person? What would be the most obvious thing someone unfamiliar with your package would try to use it for... and if they did, would they succeed after having done nothing more than read the manpage? 2. Is there any dialogue in the Tcl widgets which is a dead end, without giving guidance on what the choices actually do? (although if you read ESR's essay you might conclude that there's no point to even having widgets, since a GUI does not automatically translate into user friendliness) 3. The requirement that end-users read documentation is NOT a sign of failure for a program such as R which mostly lacks a UI... but... * Is every argument, method, and slot of every non-private object documented in the manpage *for that object* (rather than referring to some other manpage which in turn refers to another manpage, ad nauseum)? * Are the usage examples you give in the manpage simple, general, and comprehensible both to statisticians who aren't computer people and computer people who aren't statisticians? Hint: gratuitous use of functions that aren't from the package you're documenting reduces comprehensibility. * Does the documentation rely on references to hardcopy publications to explain crucial portions of the object's functionality instead of using external references as supplementary/background material? * If there is a significant number of usage scenarios where the default argument values will be inappropriate, is the user warned? * Are the manpages in sync with the current package version? 4. Do you ever find yourself using any phrase resembling "The syntax is just like it is for the S-Plus version"? 5. Does your project welcome and respond to usability feedback from non-expert users? 6. Do error messages give enough information to be able to distinguish between malformed input/arguments, platform limitations (memory, drive space, access permissions), problems in R itself, and other ("other" presumably being the real bugs)? Thank you for your patience in reading this. I don't pretend to understand the technical complexity of your work, nor your motivations for doing it. However, if you do write open source software such as Bioconductor packages, it would be logical to at least assume that you want other people to use your software. Hopefully the above considerations will assist in making that happen.