From chapmanb at arches.uga.edu Sat Mar 8 17:18:34 2003 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:21 2005 Subject: [Biopython-dev] Work on an updated biopython.org website Message-ID: <20030308221834.GA36641@arches.uga.edu> Hey all; As some of you may know, one of the things we tried to do at the hackathon in Sinapore was to do some simplification of the Bio* websites so that they are easier to keep updated. One aspect of this was introducing a shared news site where it is easy to post news for different projects (http://news.open-bio.org). With website redesign in mind, I volunteered to do some work on getting a new biopython.org site up and running (yes, I was out of my mind during volunteering). I have been working on this over the past couple of weeks and have a prototype website up at: http://evostick.agtec.uga.edu/biopython/ (be nice to this, it's just my work computer, okay). So far I've done the main index page and the download page, just to give people something to look at and give feedback on. The page is implemented using Quixote: http://www.mems-exchange.org/software/quixote/ This is a very nice (in my opinion, of course) framework for making web pages. The advantage of it are that the pages are basically made up of python code returning HTML, so I think the page makeup and everything is very easy to understand. This also allowed me to do stuff like talk to the news.open-bio.org page by XML-RPC, and theoretically could let us do more dynamic pages in the future. To get an idea of what the current pages look like, you can download the website in it's current form from: http://www.biopython.org/~chapmanb/BioWebsite-0.1.tar.gz In my mind, this can make the site a little easier to update and maintain and might ease some of the annoying HTML-typing you have to do right now. I'd love to get feedback on this from people to see what they think about what I've got. Hope everyone is having a nice weekend. Time for me to enjoy the warm Georgia weather. Brad From jchang at jeffchang.com Sat Mar 8 20:46:07 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Sat Mar 5 14:43:21 2005 Subject: [Biopython-dev] Work on an updated biopython.org website In-Reply-To: <20030308221834.GA36641@arches.uga.edu> Message-ID: Hey Brad, This looks great! Nice and clean. A few comments: - A contact email address should be on the front page somewhere. Something like, "To contact us, write biopython@biopython.org" - Is there a way to put the current version of the software (e.g. Current Release: Biopython 1.10) on the front page? This way, people will know at a glance if they're up to date. It would be best if it could be automatically sync'd with the Download page. It's no use if the version number displayed on the web page is out of date! :) - Can we simplify the links on the right side? Probably all that's necessary is: Home Download Documentation Mailing Lists Bugs CVS (contains ViewCVS, instructions to get read-only and read-write CVS) Participants (?) License and sponsors are not required. Is Participants useful? What do people think? I think it gives a more personal feel to the project, but it's not kept up to date well. Also, in the participants section, we should like what general area each participant works on, so that people will know who to ask questions to. Is a FAQ link necessary? Is it useful? It's not up to date. Maybe it should be linked from the Documentation page, if at all. - Is webteam and Chris OK with using Quixotic? Jeff On Saturday, March 8, 2003, at 02:18 PM, Brad Chapman wrote: > Hey all; > As some of you may know, one of the things we tried to do at the > hackathon in Sinapore was to do some simplification of the Bio* > websites so that they are easier to keep updated. One aspect of this > was > introducing a shared news site where it is easy to post news for > different projects (http://news.open-bio.org). > > With website redesign in mind, I volunteered to do some work on getting > a new biopython.org site up and running (yes, I was out of my mind > during volunteering). I have been working on this over the past couple > of weeks and have a prototype website up at: > > http://evostick.agtec.uga.edu/biopython/ > > (be nice to this, it's just my work computer, okay). So far I've done > the main index page and the download page, just to give people > something > to look at and give feedback on. > > The page is implemented using Quixote: > > http://www.mems-exchange.org/software/quixote/ > > This is a very nice (in my opinion, of course) framework for making web > pages. The advantage of it are that the pages are basically made up of > python code returning HTML, so I think the page makeup and everything > is > very easy to understand. This also allowed me to do stuff like talk to > the news.open-bio.org page by XML-RPC, and theoretically could let us > do > more dynamic pages in the future. > > To get an idea of what the current pages look like, you can download > the > website in it's current form from: > > http://www.biopython.org/~chapmanb/BioWebsite-0.1.tar.gz > > In my mind, this can make the site a little easier to update and > maintain and might ease some of the annoying HTML-typing you have to do > right now. > > I'd love to get feedback on this from people to see what they think > about what I've got. > > Hope everyone is having a nice weekend. Time for me to enjoy the warm > Georgia weather. > Brad > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From idoerg at burnham.org Sun Mar 9 23:01:58 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Sat Mar 5 14:43:21 2005 Subject: [Biopython-dev] Work on an updated biopython.org website In-Reply-To: Message-ID: Nice going Brad!!! Crispy-clean page. Re: Jeff's questions about participants: yes, I think we should have the link on the front page, both for the "personal feel" reason Jeff mentioned, and as a bit of an acknowledgement reward (=="who to blame for the bugs") for contributors. Best, Iddo -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://bioinformatics.ljcrf.edu/~iddo From chapmanb at arches.uga.edu Mon Mar 10 11:48:27 2003 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:21 2005 Subject: [Biopython-dev] Work on an updated biopython.org website In-Reply-To: References: <20030308221834.GA36641@arches.uga.edu> Message-ID: <20030310164827.GB40178@arches.uga.edu> Jeff and Iddo; Thanks for the feedback. I'm glad it looks alright -- I'm definitely no web design genius; thank god for Chris getting the open-bio page up first! > A few comments: > > - A contact email address should be on the front page somewhere. > Something like, "To contact us, write biopython@biopython.org" > > - Is there a way to put the current version of the software (e.g. > Current Release: Biopython 1.10) on the front page? This way, people > will know at a glance if they're up to date. It would be best if it > could be automatically sync'd with the Download page. It's no use if > the version number displayed on the web page is out of date! :) Good ideas. I added these to the front page. Keeping the front page version synched with the download information is pretty easy with the Quixote framework. For making a new release you should just need to modify the version number of the download page, specify the download files available in a python list and it should be all set. Hopefully this'll make it easier for us to keep everything simple and up to date. > > - Can we simplify the links on the right side? Probably all that's > necessary is: > Home > Download > Documentation > Mailing Lists > Bugs > CVS (contains ViewCVS, instructions to get read-only and read-write > CVS) > Participants (?) Sounds good. The simpler the better. > Is Participants useful? What do people think? I think it gives a more > personal feel to the project, but it's not kept up to date well. Also, > in the participants section, we should like what general area each > participant works on, so that people will know who to ask questions to. I agree with Iddo. I like the Participants page. What I'd like to do is make this dynamic so that people can add themselves with a form right on the web. We'd just have some sort of simple password so random people on the web can't be jerks, and then everyone can be responsible for themselves. I'll solicit more feedback on what people want on the page when I get to that. > Is a FAQ link necessary? Is it useful? It's not up to date. Maybe it > should be linked from the Documentation page, if at all. We should be keeping a FAQ, I think, but just like all the other docs we need someone to maintain it. I think the best idea is to just link to it from the Documentation page. BTW, I think we should just get rid of the wiki. It doesn't really seem to get much use and is just another thing that will get out of date. I love wikis, but stay simple. Stay simple. > - Is webteam and Chris OK with using Quixotic? That I don't know. This is one reason I wrote about it, cause I don't want to go too far with it and find out people don't like it for one reason or another. It's pretty easy to install. All we'd need to get the current page up on biopython.org is a working python, quixote, mxDateTime and HTMLgen. Shouldn't be too difficult. It just uses standard cgi scripts, so hopefully it'll be pretty easy to maintain and things. Chris? Whadda you all think? Thanks again for the feedback! Brad From biopython-bugs at bioperl.org Wed Mar 12 03:14:16 2003 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:21 2005 Subject: [Biopython-dev] Notification: incoming/125 Message-ID: <200303120814.h2C8EGQw015225@pw600a.bioperl.org> JitterBug notification new message incoming/125 Message summary for PR#125 From: "" Subject: look twenty years younger m xlo z sjewyk s Date: Wed, 12 Mar 03 02:56:19 GMT 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From aiocicarelli@msn.com Wed Mar 12 03:14:15 2003 Received: from BA018097.user.veloxzone.com.br (BA018097.user.veloxzone.com.br [200.164.18.97]) by pw600a.bioperl.org (8.12.6/8.12.6) with SMTP id h2C8DhQw015184 for ; Wed, 12 Mar 2003 03:13:59 -0500 Received: from h7rid.gd [182.145.157.75] by BA018097.user.veloxzone.com.br with ESMTP id UWCTJ; Wed, 12 Mar 03 02:59:19 +0400 Received: from ewr58..bg [203.91.36.16] by 182.145.157.75 with ESMTP id EHPHQ; Wed, 12 Mar 03 02:56:19 +0400 Message-ID: > From: "" To: biopython-bugs@bioperl.org Subject: look twenty years younger m xlo z sjewyk s Date: Wed, 12 Mar 03 02:56:19 GMT X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="3.CC6_B_A.0.0BF_9F" X-Spam-Warning: SpamAssassin says this message is SPAM X-Spam-Status: Yes X-Spam-Report: SPAM: ---- Start SpamAssassin results SPAM: 5.70 hits, 5 required; SPAM: * 1.3 -- From: does not include a real name SPAM: * 0.2 -- X-Mailer header indicates a non-spam MUA (Outlook Express) SPAM: * 0.0 -- Message-Id is not valid, according to RFC 2822 SPAM: * 0.8 -- BODY: Spam phrases score is 00 to 01 (low) SPAM: [score: 0] SPAM: * 0.3 -- BODY: FONT Size +2 and up or 3 and up SPAM: * 0.3 -- BODY: HTML font face is not a commonly used face SPAM: * 0.2 -- BODY: HTML font color is blue SPAM: * 0.7 -- RAW: Message text in HTML without specified charset SPAM: * 1.4 -- Date: is 3 to 6 hours after Received: date SPAM: * 0.5 -- Message has X-MSMail-Priority, but no X-MimeOLE SPAM: SPAM: ---- End of SpamAssassin results X-Spam-Level: ***** (5.7) X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) This is a multi-part message in MIME format. --3.CC6_B_A.0.0BF_9F Content-Type: text/html Content-Transfer-Encoding: quoted-printable 
  

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t jnegz --3.CC6_B_A.0.0BF_9F-- From bugzilla-daemon at cvs.open-bio.org Wed Mar 12 12:53:36 2003 From: bugzilla-daemon at cvs.open-bio.org (bugzilla-daemon@cvs.open-bio.org) Date: Sat Mar 5 14:43:21 2005 Subject: [Biopython-dev] [Bug 1409] New: Problems with Martel and setup.py Message-ID: <200303121753.h2CHraa07528@cvs.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1409 Summary: Problems with Martel and setup.py Product: Biopython Version: Not Applicable Platform: All OS/Version: All Status: NEW Severity: normal Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: jchang@biopython.org This is against the CVS version. I received an email from Dan Rubin that outlined the problem: - Martel installed at li/python22/site-packages - python setup.py generates AttributeError: "module" object has no attribute 'AnyEol' - after removing Martel from site-packages, builds correctly - python setup.py install tells you that you need Martel first - after ignoring message, Martel installed anyway 2 problems: 1. Attribute Error should not be raised 2. messages are confusing ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From idoerg at burnham.org Thu Mar 13 12:44:53 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Sat Mar 5 14:43:21 2005 Subject: [Biopython-dev] CVS again: Message-ID: <3E70C395.7030508@burnham.org> What is the current CVS address? My command line hangs on: % setnev CVS_RSH 'ssh' % cvs -d :ext:idoerg@dev.open-bio.org:/home/repository/biopython \ checkout biopython (Catastrophic event on disk.. need to recover cvs. Boo hoo) best, I. -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://bioinformatics.ljcrf.edu/~iddo From bugzilla-daemon at cvs.open-bio.org Sun Mar 16 13:06:49 2003 From: bugzilla-daemon at cvs.open-bio.org (bugzilla-daemon@cvs.open-bio.org) Date: Sat Mar 5 14:43:21 2005 Subject: [Biopython-dev] [Bug 1411] New: t_coffee *.aln reading Message-ID: <200303161806.h2GI6nQ22086@cvs.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1411 Summary: t_coffee *.aln reading Product: Biopython Version: Not Applicable Platform: All URL: http://cvs.biopython.org/cgi- bin/viewcvs/viewcvs.cgi/biopython/Bio/Clustalw/clustal_f ormat.py?rev=1.5&cvsroot=biopython&content- type=text/vnd.viewcvs-markup OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: ktdiedrich@yahoo.com The Bio.Clustalw.clustal_format file cannot read t_coffee alignments which are the same a Clustalw alignments except for the header. By making the regular expression for the header more general both can be read. A diff -c that makes Bio.Clustalw.clustal_format work for both is: *** clustal_format.py Sun Mar 16 11:09:29 2003 --- clustal_format.py.orig Sun Mar 16 10:12:50 2003 *************** *** 24,30 **** header = Martel.Group("header", Martel.Str("CLUSTAL ") + ! Martel.Re(".+") + Martel.MaxRepeat(Martel.AnyEol(), 0, 3)) seq_id = Martel.Group("seq_id", --- 24,33 ---- header = Martel.Group("header", Martel.Str("CLUSTAL ") + ! Martel.Re("[X|W]") + ! Martel.Re("[ (]+") + ! version + ! Martel.Str(") multiple sequence alignment") + Martel.MaxRepeat(Martel.AnyEol(), 0, 3)) seq_id = Martel.Group("seq_id", ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at cvs.open-bio.org Mon Mar 17 15:01:34 2003 From: bugzilla-daemon at cvs.open-bio.org (bugzilla-daemon@cvs.open-bio.org) Date: Sat Mar 5 14:43:21 2005 Subject: [Biopython-dev] [Bug 1411] t_coffee *.aln reading Message-ID: <200303172001.h2HK1Y414364@cvs.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1411 chapmanb@arches.uga.edu changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Additional Comments From chapmanb@arches.uga.edu 2003-03-17 15:01 ------- Fixed in CVS with the patch provided. Thanks! ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From jongud at hi.is Tue Mar 18 09:41:01 2003 From: jongud at hi.is (jongud@hi.is) Date: Sat Mar 5 14:43:21 2005 Subject: [Biopython-dev] Biopython: question regarding example code Message-ID: <1391.157.157.143.198.1047998461.squirrel@webmail.hi.is> Hello My name is J?n Gu?mundsson and I am studying computer science at the University of Iceland. I have been looking at biopython and reading the tutorial and cookbook. There are good examples there about what can be done with it but is there some sort of white paper or overview of what is currently implemented with biopython. Like for example overview of all the databases that biopython can be used to work with. Also I tried running the examples that come with the distribution but could not run the pubmed_search.py program. The output was: [jongud@oracle examples]$ python pubmed_search.py Traceback (most recent call last): File "pubmed_search.py", line 6, in ? from Bio.Medline import PubMed ImportError: cannot import name PubMed I tried changing the import lines in the code to something else that might work but nothing worked. I was running it on linux machine and the other examples worked. The distribution of biopython that was set up was 1.10. Regards J?n From chapmanb at arches.uga.edu Tue Mar 18 09:58:09 2003 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:21 2005 Subject: [Biopython-dev] Biopython: question regarding example code In-Reply-To: <1391.157.157.143.198.1047998461.squirrel@webmail.hi.is> References: <1391.157.157.143.198.1047998461.squirrel@webmail.hi.is> Message-ID: <20030318145809.GA1776@arches.uga.edu> Hi J?n; > I have been looking at biopython and reading the tutorial and cookbook. > There are good examples there about what can be done with it but is there > some sort of white paper or overview of what is currently implemented with > biopython. Like for example overview of all the databases that biopython > can be used to work with. The documentation you can find at http://www.biopython.org/wiki/html/BioPython/BiopythonCode.html is what we've got. I am currently working on a rewrite of the docs as I know a lot of errors have crept in (but first I have to finish the web pages -- hard workin' over here :-) since they were written. I'm not sure exactly what you are looking for, but there are also a couple of online courses with nice Biopython introductions linked to from the above page which might be worth checking out. > Also I tried running the examples that come with the distribution but > could not run the pubmed_search.py program. The output was: > > [jongud@oracle examples]$ python pubmed_search.py > Traceback (most recent call last): > File "pubmed_search.py", line 6, in ? > from Bio.Medline import PubMed > ImportError: cannot import name PubMed > > I tried changing the import lines in the code to something else that might > work but nothing worked. I was running it on linux machine and the other > examples worked. The distribution of biopython that was set up was 1.10. This is my fault -- an out of date import. You need to change the import line to: from Bio import PubMed and it should work fine. Thanks for reporting this -- I've fixed it in CVS. I know there are other places in the docs and examples where import errors may have crept in -- I'm working on tracking them all down. Sorry about some of the out-of-dateness of the documentation -- I definitely welcome patches or reports of mistakes as we're trying to get them cleaned up. Always happy to have people trying out Biopython! Thanks again for the report! Brad From biopython-bugs at bioperl.org Tue Mar 18 20:27:17 2003 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:21 2005 Subject: [Biopython-dev] Notification: incoming/126 Message-ID: <200303190127.h2J1RHGg028062@pw600a.bioperl.org> JitterBug notification new message incoming/126 Message summary for PR#126 From: =?GB2312?B?vsXW3c7v18rQxc izfg=?= Subject: none Date: Tue, 18 Mar 2003 20:27:09 -0500 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From remove@jzwx.com Tue Mar 18 20:27:16 2003 Received: from jzwx.com ([61.183.173.88]) by pw600a.bioperl.org (8.12.6/8.12.6) with ESMTP id h2J1R3Gh028057 for ; Tue, 18 Mar 2003 20:27:09 -0500 Date: Tue, 18 Mar 2003 20:27:09 -0500 Message-Id: <200303190127.h2J1R3Gh028057@pw600a.bioperl.org> From: =?GB2312?B?vsXW3c7v18rQxc+izfg=?= Subject: =?GB2312?B?YmlvcHl0aG9uLWJ1Z3MsxPq6w6OhttTE+sn60uLT0LDv1vqjrLb4x9K++LbU?= =?GB2312?B?w+K30aOh?= To: biopython-bugs@bioperl.org Content-Type: text/html;charset="GB2312" Date: Wed, 19 Mar 2003 09:28:06 +0800 X-Priority: 3 X-Mailer: Microsoft Outlook Express 6.00.2600.0000 九州物资信息网--首页

http://www.jzwx.com                     首页 | 会员注册 | 客户服务 ====> MESSAGE TRUNCATED AT 8192 <==== From chapmanb at uga.edu Wed Mar 19 17:44:23 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:21 2005 Subject: [Biopython-dev] "Final" biopython website for your inspection Message-ID: <20030319224423.GB5057@uga.edu> Hey all; Based on the feedback I got on the first version of a new biopython website that I sent out, I figured that a few people liked it and it didn't make anyone retch -- so I went ahead and finished what I consider a "final" biopython website I'd be willing to put up as the main site. The site, for your fine inspection, is up at: http://evostick.agtec.uga.edu/biopython/ It contains all of the content we talked about last go at the site. This is less static text then before, which I think is a good thing since it's very hard to keep all of that updated. I've also added a Participants page that can be edited online (add yourself, delete yourself, edit your information). It uses a single username and password to allow you to login and do the editing, to provide enough "security" that someone especially annoying can't delete everyone or do other mischievous things. I'd encourage people to add themselves and play around with it. The login name is 'biopython' and the password is 'user.' I'd love to get feedback on this and get it in a final form so that we can get it going at biopython.org. Please play around with it and let with it and let me know any thoughts. Doing the site was a good experience for me as I haven't done much with (semi-)interactive sites before -- mmmm, sessions, cookies; lots of learning for me. Now I'm ready to leave you suckas in the dust and embark on a wondeful new life of making big coin designing websites :-). Brad From jchang at smi.stanford.edu Wed Mar 19 18:13:33 2003 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:21 2005 Subject: [Biopython-dev] "Final" biopython website for your inspection In-Reply-To: <20030319224423.GB5057@uga.edu> Message-ID: <67CA2F69-5A60-11D7-9A11-000A956845CE@smi.stanford.edu> Hey, super-cool job! Looks great! Looks ready to go to me. One thing: under Documentation, "Online courses" should be changed to "Course Notes" or "Online Course Notes" or something, to prevent giving people the idea that we teach courses online! Jeff On Wednesday, March 19, 2003, at 02:44 PM, Brad Chapman wrote: > Hey all; > Based on the feedback I got on the first version of a new biopython > website that I sent out, I figured that a few people liked it and it > didn't make anyone retch -- so I went ahead and finished what I > consider > a "final" biopython website I'd be willing to put up as the main site. > > The site, for your fine inspection, is up at: > > http://evostick.agtec.uga.edu/biopython/ > > It contains all of the content we talked about last go at the site. > This > is less static text then before, which I think is a good thing since > it's very hard to keep all of that updated. > > I've also added a Participants page that can be edited online (add > yourself, delete yourself, edit your information). It uses a single > username and password to allow you to login and do the editing, to > provide enough "security" that someone especially annoying can't delete > everyone or do other mischievous things. I'd encourage people to add > themselves and play around with it. The login name is 'biopython' and > the password is 'user.' > > I'd love to get feedback on this and get it in a final form so that we > can get it going at biopython.org. Please play around with it and let > with it and let me know any thoughts. > > Doing the site was a good experience for me as I haven't done much with > (semi-)interactive sites before -- mmmm, sessions, cookies; lots of > learning for me. Now I'm ready to leave you suckas in the dust and > embark on a wondeful new life of making big coin designing websites > :-). > > Brad > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From katel at worldpath.net Wed Mar 19 19:56:19 2003 From: katel at worldpath.net (katel@worldpath.net) Date: Sat Mar 5 14:43:21 2005 Subject: [Biopython-dev] Final biopython website for your inspection Message-ID: <265000-22003342005619544@M2W028.mail2web.com> Its a great plain vanilla site but I think it needs something to entice new visitors. Like colored borders, fonts, graphic clips of proteins, scientists at work, conferences and the logo to add pizazz. Cayte Original Message: ----------------- From: Jeffrey Chang jchang@smi.stanford.edu Date: Wed, 19 Mar 2003 15:13:33 -0800 To: chapmanb@uga.edu, biopython-dev@biopython.org Subject: Re: [Biopython-dev] "Final" biopython website for your inspection Hey, super-cool job! Looks great! Looks ready to go to me. One thing: under Documentation, "Online courses" should be changed to "Course Notes" or "Online Course Notes" or something, to prevent giving people the idea that we teach courses online! Jeff On Wednesday, March 19, 2003, at 02:44 PM, Brad Chapman wrote: > Hey all; > Based on the feedback I got on the first version of a new biopython > website that I sent out, I figured that a few people liked it and it > didn't make anyone retch -- so I went ahead and finished what I > consider > a "final" biopython website I'd be willing to put up as the main site. > > The site, for your fine inspection, is up at: > > http://evostick.agtec.uga.edu/biopython/ > > It contains all of the content we talked about last go at the site. > This > is less static text then before, which I think is a good thing since > it's very hard to keep all of that updated. > > I've also added a Participants page that can be edited online (add > yourself, delete yourself, edit your information). It uses a single > username and password to allow you to login and do the editing, to > provide enough "security" that someone especially annoying can't delete > everyone or do other mischievous things. I'd encourage people to add > themselves and play around with it. The login name is 'biopython' and > the password is 'user.' > > I'd love to get feedback on this and get it in a final form so that we > can get it going at biopython.org. Please play around with it and let > with it and let me know any thoughts. > > Doing the site was a good experience for me as I haven't done much with > (semi-)interactive sites before -- mmmm, sessions, cookies; lots of > learning for me. Now I'm ready to leave you suckas in the dust and > embark on a wondeful new life of making big coin designing websites > :-). > > Brad > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev _______________________________________________ Biopython-dev mailing list Biopython-dev@biopython.org http://biopython.org/mailman/listinfo/biopython-dev -------------------------------------------------------------------- mail2web - Check your email from the web at http://mail2web.com/ . From dig.list at nm.ru Thu Mar 20 00:31:01 2003 From: dig.list at nm.ru (DIG) Date: Sat Mar 5 14:43:21 2005 Subject: [Biopython-dev] "Final" biopython website for your inspection In-Reply-To: <20030319224423.GB5057@uga.edu>; from "Brad Chapman" on Wed, Mar 19, 2003 at 05:44:23PM References: <20030319224423.GB5057@uga.edu> Message-ID: <20030319233101.H24015@lifebook> Hi, Brad Chapman ! On Wed, Mar 19, 2003 at 05:44:23PM -0500, Brad Chapman wrote: [...] > The site, for your fine inspection, is up at: > > http://evostick.agtec.uga.edu/biopython/ [...] (1) Shouldn't this line (#105) BioSQL / OBDA
be like this BioSQL / OBDA
? (2) There are some
and
mixture in the source. May be it is better to have one kind of
? (3) I have some doubts about DOCTYPE ... This is because w3.org's validator give me only 9 errors, if I specify this page as being HTML-4.01 Transitional [1]. And it gives more than 40 errors, if I use autodetect [2], which gives me XHTML-1.0 Transitional. [1] http://validator.w3.org/check?uri=http%3A%2F%2Fevostick.agtec.uga.edu%2Fbiopython%2F&charset=%28detect+automatically%29&doctype=HTML+4.01+Transitional [2] http://validator.w3.org/check?uri=http%3A%2F%2Fevostick.agtec.uga.edu%2Fbiopython%2F&charset=%28detect+automatically%29&doctype=%28detect+automatically%29 (4) I have also one suggestion. Wouldn't this page look more "finished" if at the end of page there were some kind of indication, that it is the end of page ? I was thinking about standard things, like (C) sign, date of last modification or even $Id$ string. What do you think ? Besides that, this is very clean and nice design. Best regards, -- DIG (Dmitri I GOULIAEV) 26A0 E4D5 AB3F C2D4 0112 66CD 4343 C0AF 63A6 C649 From Yves.Bastide at irisa.fr Thu Mar 20 08:30:01 2003 From: Yves.Bastide at irisa.fr (Yves Bastide) Date: Sat Mar 5 14:43:21 2005 Subject: [Biopython-dev] "Final" biopython website for your inspection In-Reply-To: <20030319224423.GB5057@uga.edu> References: <20030319224423.GB5057@uga.edu> Message-ID: <3E79C259.8070203@irisa.fr> Brad Chapman wrote: > Hey all; > Based on the feedback I got on the first version of a new biopython > website that I sent out, I figured that a few people liked it and it > didn't make anyone retch -- so I went ahead and finished what I consider > a "final" biopython website I'd be willing to put up as the main site. > > The site, for your fine inspection, is up at: > > http://evostick.agtec.uga.edu/biopython/ > Nice! Except for the open-bio.org/styles-site.css style sheet designed for IE and which prescribes too small fonts for other browsers... > > Brad yves From biopython-bugs at bioperl.org Thu Mar 20 22:08:46 2003 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:21 2005 Subject: [Biopython-dev] Notification: incoming/127 Message-ID: <200303210308.h2L38kGg018535@pw600a.bioperl.org> JitterBug notification new message incoming/127 Message summary for PR#127 From: =?GB2312?B?vsXW3c7v18rQxc izfg=?= Subject: none Date: Thu, 20 Mar 2003 22:08:40 -0500 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From remove@jzwx.com Thu Mar 20 22:08:45 2003 Received: from jzwx.com ([61.183.178.101]) by pw600a.bioperl.org (8.12.6/8.12.6) with ESMTP id h2L38aGh018531 for ; Thu, 20 Mar 2003 22:08:40 -0500 Date: Thu, 20 Mar 2003 22:08:40 -0500 Message-Id: <200303210308.h2L38aGh018531@pw600a.bioperl.org> From: =?GB2312?B?vsXW3c7v18rQxc+izfg=?= Subject: =?GB2312?B?YmlvcHl0aG9uLWJ1Z3MsxPq6w6OhttTE+sn60uLT0LDv1vqjrLb4x9K++LbU?= =?GB2312?B?w+K30aOh?= To: biopython-bugs@bioperl.org Content-Type: text/html;charset="GB2312" Date: Fri, 21 Mar 2003 11:09:35 +0800 X-Priority: 3 X-Mailer: FoxMail 3.11 Release [cn] 九州物资信息网--首页

http://www.jzwx.com                     首页 | 会员注册 | 客户服务 | References: <20030319224423.GB5057@uga.edu> <67CA2F69-5A60-11D7-9A11-000A956845CE@smi.stanford.edu> Message-ID: <20030321161926.GD9578@uga.edu> Hey everyone; Thanks for the feedback. I'll try to respond to everyone's comments in one mail. Jeff: > Looks ready to go to me. One thing: under Documentation, "Online > courses" should be changed to "Course Notes" or "Online Course Notes" > or something, to prevent giving people the idea that we teach courses > online! Good point :-). Fixed. Iddo: > Do we want license terms on the front page, or within a 1-click radius > of the front page? Personally, I'd rather just have the license included in the distribution and leave it at that. Less pages and it's really not too interesting to look at (do whatever you want with the code, don't blame us). Do other people think we need it? Yves: > Nice! Except for the open-bio.org/styles-site.css style sheet designed > for IE and which prescribes too small fonts for other browsers... Really? Ugh. Which browsers do you find it looking bad in? I checked it on IE, Mozilla, Netscape 4.7 and Galeon (which is actually the browser I use) and all looked okay. I was hoping this covered the mozilla/ie front reasonably well. Let me know and I can try to figure that; CSS isn't really my speciality -- I just grabbed the open-bio one so we'd have the same "look and feel." Cayte: > Its a great plain vanilla site but I think it needs something to entice > new visitors. Like colored borders, fonts, graphic clips of proteins, > scientists at work, conferences and the logo to add pizazz. I have to admit I don't like pizzaz things like moving graphics and all, but I would like to put a logo on there if anyone wants to design one. We have Iddo's which I use sometimes for talks, but he doesn't like to take credit for it :-). If we have any graphic design/artist types who want to generate one I would be very into including it. Something nice that fit next on the top of the page would be sweet. Dmitri; > (1) Shouldn't this line (#105) > > BioSQL / OBDA
> > be like this > > BioSQL / OBDA
> > ? Actually, ODBA is a separate thing from BioSQL (I know, it's confusing). BioSQL is basically "storing sequences and features in an SQL database" and OBDA is "standardized ways to access biological databases." I think OBDA will have it's own web site soon, then this'll all be cleared up. > (2) There are some
and
mixture in the source. May be > it is better to have one kind of
? Excellent point. They are all
s now since I decided to go with the xhtml. > (3) I have some doubts about DOCTYPE ... This is because w3.org's validator Doh, validating. Thanks for reminding me. I fixed everything up so we validate against the specified XHTML doctype. Many thanks for reminding me of this. > (4) I have also one suggestion. Wouldn't this page look more "finished" > if at the end of page there were some kind of indication, that it is the > end of page ? I was thinking about standard things, like (C) sign, date > of last modification or even $Id$ string. What do you think ? Good idea. Once I get this stuff into CVS I'll try to get those fancy datestamp things working (I'll have to look that up) and add a Last Modified tag to the bottom of all the pages like we have right now. Whew. I think that's all the concerns. What do people think -- should I move on getting this up? I can write Chris about permissions and things and we can pick a night and I'll get it done and just do it. Thanks again for all the feedback! Brad From jchang at jeffchang.com Mon Mar 24 18:04:55 2003 From: jchang at jeffchang.com (Jeffrey Chang) Date: Sat Mar 5 14:43:21 2005 Subject: [Biopython-dev] "Final" biopython website for your inspection In-Reply-To: <20030321161926.GD9578@uga.edu> Message-ID: <07170B90-5E4D-11D7-8F00-000A956845CE@jeffchang.com> > [Brad] > Whew. I think that's all the concerns. What do people think -- should I > move on getting this up? I can write Chris about permissions and things > and we can pick a night and I'll get it done and just do it. Go for it! Let me know if I can help with it. Jeff