Comments on: Three of many possible reasons why I haven’t responded to your email about HMMER. http://selab.janelia.org/people/eddys/blog/?p=289 The Eddy lab: genome sequence analysis Thu, 12 Aug 2010 11:54:36 -0400 http://wordpress.org/?v=2.8.4 hourly 1 By: Friday SNPpets | The OpenHelix Blog http://selab.janelia.org/people/eddys/blog/?p=289&cpage=1#comment-9884 Friday SNPpets | The OpenHelix Blog Fri, 02 Apr 2010 05:03:14 +0000 http://selab.janelia.org/people/eddys/blog/?p=289#comment-9884 [...] Eddy on HMMR help, reading documentation, and more in his blog post at Cryptogenomicon. [...] [...] Eddy on HMMR help, reading documentation, and more in his blog post at Cryptogenomicon. [...]

]]> By: German Leparc http://selab.janelia.org/people/eddys/blog/?p=289&cpage=1#comment-9417 German Leparc Mon, 22 Mar 2010 17:27:01 +0000 http://selab.janelia.org/people/eddys/blog/?p=289#comment-9417 Btw, Sean, How do I compile HMMR3 on an old Altos 586 Xenix machine? ;) I support the idea of a forum. SEQanswers, as Matt has suggested, is an excellent place and I have used it extensively to exchange with authors and users. In fact, I'm convinced questions about software should be handled strictly on a forum instead of email - reduces redundacy, is searchable, and users can help each other answer questions. I don't like mailing lists - too annoying to deal with. Greetings from Vienna, German Btw, Sean, How do I compile HMMR3 on an old Altos 586 Xenix machine? ;)

I support the idea of a forum. SEQanswers, as Matt has suggested, is an excellent place and I have used it extensively to exchange with authors and users. In fact, I’m convinced questions about software should be handled strictly on a forum instead of email – reduces redundacy, is searchable, and users can help each other answer questions.

I don’t like mailing lists – too annoying to deal with.

Greetings from Vienna,
German

]]> By: Marshall Hampton http://selab.janelia.org/people/eddys/blog/?p=289&cpage=1#comment-9416 Marshall Hampton Mon, 22 Mar 2010 16:44:56 +0000 http://selab.janelia.org/people/eddys/blog/?p=289#comment-9416 The Sage project (math, not sequencing) has a very active google group which has worked well for us overall: http://groups.google.com/group/sage-support Maybe the SEQAnswers people would make a HMMER forum for you if you asked - that would be a good way to leverage the expertise over there. The Sage project (math, not sequencing) has a very active google group which has worked well for us overall:
http://groups.google.com/group/sage-support

Maybe the SEQAnswers people would make a HMMER forum for you if you asked – that would be a good way to leverage the expertise over there.

]]> By: Deepak http://selab.janelia.org/people/eddys/blog/?p=289&cpage=1#comment-9245 Deepak Fri, 19 Mar 2010 02:18:53 +0000 http://selab.janelia.org/people/eddys/blog/?p=289#comment-9245 vBulletin in particular is definitely preferable to Google Groups which has some issues as mentioned above. Another really nice option is Vanilla http://vanillaforums.org/ vBulletin in particular is definitely preferable to Google Groups which has some issues as mentioned above.

Another really nice option is Vanilla

http://vanillaforums.org/

]]> By: Matt http://selab.janelia.org/people/eddys/blog/?p=289&cpage=1#comment-9121 Matt Mon, 15 Mar 2010 21:12:47 +0000 http://selab.janelia.org/people/eddys/blog/?p=289#comment-9121 I've read that Google Groups have some pervasive problems, see: http://ejohn.org/blog/google-groups-is-dead/ The comments there mention some alternatives; I think the jQuery team went with Zoho Discussions. Other forums mentioned are phpBB, vBulletin, and FluxBB. Here's a nifty comparison tool (bordering on overwhelming): http://www.forum-software.org/forum-comparator/fluxbb-vs-mybb-vs-phpbb3-vs-zoho-discussions Maybe such a message board would trade one headache for another (spam moderation, blech). I see the Genetic Software Forum closed up shop in the past year partially for those reasons: http://gsf.gc.ucdavis.edu/viewtopic.php?f=1&t=2876 SEQAnswers is a vBulletin-powered forum that seems active: http://seqanswers.com/forums/index.php Good luck. I’ve read that Google Groups have some pervasive problems, see:

http://ejohn.org/blog/google-groups-is-dead/

The comments there mention some alternatives; I think the jQuery team went with Zoho Discussions. Other forums mentioned are phpBB, vBulletin, and FluxBB. Here’s a nifty comparison tool (bordering on overwhelming):

http://www.forum-software.org/forum-comparator/fluxbb-vs-mybb-vs-phpbb3-vs-zoho-discussions

Maybe such a message board would trade one headache for another (spam moderation, blech). I see the Genetic Software Forum closed up shop in the past year partially for those reasons:

http://gsf.gc.ucdavis.edu/viewtopic.php?f=1&t=2876

SEQAnswers is a vBulletin-powered forum that seems active:

http://seqanswers.com/forums/index.php

Good luck.

]]> By: Sean Eddy http://selab.janelia.org/people/eddys/blog/?p=289&cpage=1#comment-9119 Sean Eddy Mon, 15 Mar 2010 20:13:46 +0000 http://selab.janelia.org/people/eddys/blog/?p=289#comment-9119 Any examples of a well-running Google Group? The first few I looked at look disused, uninviting; a bad part of town. Any examples of a well-running Google Group? The first few I looked at look disused, uninviting; a bad part of town.

]]> By: Morgan Langille http://selab.janelia.org/people/eddys/blog/?p=289&cpage=1#comment-9117 Morgan Langille Mon, 15 Mar 2010 19:21:11 +0000 http://selab.janelia.org/people/eddys/blog/?p=289#comment-9117 Yes, I have to agree with Matt. Set up a Google Group (it takes < 5 minutes), and post the mailing list for that group on the hmmer site instead of your own. To be honest, the couple of times I have emailed you (which you did respond to by the way) I checked to make sure I shouldn't be sending it to some hmmer specific mailing list. The biggest benefit is that you might get a few other users actually answering the questions for you. Of course this means that the correspondence on hmmer would be more open and transparent, but I think that would a good thing. Also, it would avoid you getting the same email more than once about such an such a bug. Yes, I have to agree with Matt. Set up a Google Group (it takes < 5 minutes), and post the mailing list for that group on the hmmer site instead of your own. To be honest, the couple of times I have emailed you (which you did respond to by the way) I checked to make sure I shouldn't be sending it to some hmmer specific mailing list.

The biggest benefit is that you might get a few other users actually answering the questions for you. Of course this means that the correspondence on hmmer would be more open and transparent, but I think that would a good thing. Also, it would avoid you getting the same email more than once about such an such a bug.

]]> By: Sean Eddy http://selab.janelia.org/people/eddys/blog/?p=289&cpage=1#comment-9116 Sean Eddy Mon, 15 Mar 2010 19:18:10 +0000 http://selab.janelia.org/people/eddys/blog/?p=289#comment-9116 I have, but haven't gotten as far as doing anything. I'm not a huge fan of mailing lists (see above) but a forum sounds like a good idea. Do you (or does anyone else) have suggestions for setting one up? Looks like XKCD's forum is running on phpBB, and that looks pretty functional. I have, but haven’t gotten as far as doing anything. I’m not a huge fan of mailing lists (see above) but a forum sounds like a good idea. Do you (or does anyone else) have suggestions for setting one up? Looks like XKCD’s forum is running on phpBB, and that looks pretty functional.

]]> By: Matt http://selab.janelia.org/people/eddys/blog/?p=289&cpage=1#comment-9112 Matt Mon, 15 Mar 2010 18:02:19 +0000 http://selab.janelia.org/people/eddys/blog/?p=289#comment-9112 Sean, have you considered setting up a forum or mailing list so users could answer each others' questions? MrBayes and PAML are two examples of software I've used with reasonably active lists, and I'm guessing that HMMER has a user base big enough to support this approach. Sean, have you considered setting up a forum or mailing list so users could answer each others’ questions? MrBayes and PAML are two examples of software I’ve used with reasonably active lists, and I’m guessing that HMMER has a user base big enough to support this approach.

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