From rmb32 at cornell.edu Sun Aug 1 15:17:14 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Sun, 01 Aug 2010 12:17:14 -0700 Subject: [Open-bio-l] GMOD Evo Hackathon Open Call for Participation Message-ID: <4C55C83A.3060700@cornell.edu> We are seeking participants for the GMOD Tools for Evolutionary Biology Hackathon, held November 8-12, 2010 at the US National Evolutionary Synthesis Center (NESCent) in Durham, NC. This hackathon targets three critical gaps in the capabilities of the GMOD toolbox that currently limit its utility for evolutionary research: 1. Visualization of comparative genomics data 2. Visualization of phylogenetic data and trees 3. Support for population diversity and phenotype data If you are interested in these areas and have relevant expertise, you are strongly encouraged to apply. Relevant areas of expertise include more than just software development: if you are a GMOD power user, visualization guru, domain expert (comparative, phylogenetics, population, ...), or documentation wizard, then your skills are needed! How To Apply: Fill out the online application form at http://bit.ly/gmodevohack. Applications are due August 25. About GMOD: GMOD is an intercompatible suite of open-source software components for storing, managing, analyzing, and visualizing genome-scale data. GMOD includes many widely-used software components: GBrowse and JBrowse, both genome viewers; GBrowse_syn, a comparative genomics viewer; Chado, a generic and modular database schema; CMap, a comparative map viewer; as well as many other components including Apollo, MAKER, BioMart, InterMine, and Galaxy. We hope to extend the functionality of existing GMOD components, and integrate new components as well. About Hackathons: A hackathon is an intense event at which a group of programmers with different backgrounds and skills collaborate hands-on and face-to-face to develop working code that is of utility to the community as a whole. The mix of people will include domain experts and computer-savvy end-users. More details about the event, its motivation, organization, procedures, and attendees, as well as URLs to the hackathon and related websites are included below. Sincerely, The GMOD EvoHack Organizing Committee (and project affiliations as relevant): Nicole Washington, Chair (LBNL, modENCODE, Phenote) Robert Buels (SGN, Chado NatDiv) Scott Cain (OICR, GMOD) Dave Clements (NESCent, GMOD) Hilmar Lapp (NESCent, Phenoscape, Chado NatDiv) Sheldon McKay (University of Arizona, iPlant, GBrowse_syn) ----------------------------- About the GMOD Evo Hackathon Overview We are organizing a hackathon to fill critical gaps in the capabilities of the Generic Model Organism Database (GMOD) toolbox that currently limit its utility for evolutionary research. Specifically, we will focus on tools for 1) viewing comparative genomics data; 2) visualizing phylogenomic data; and 3) supporting population diversity data and phenotype annotation. The event will be hosted at NESCent and bring together a group of about 20+ software developers, end-user representatives, and documentation experts who would otherwise not meet. The participants will include key developers of GMOD components that currently lack features critical for emerging evolutionary biology research, developers of informatics tools in evolutionary research that lack GMOD integration, and informatics-savvy biologists who can represent end-user requirements. The event will provide a unique opportunity to infuse the GMOD developer community with a heightened awareness of unmet needs in evolutionary biology that GMOD components have the potential to fill, and for tool developers in evolutionary biology to better understand how best to extend or integrate with already existing GMOD components. Before the Event Discussion of ideas and sometimes even design actually starts well before the hackathon, on mailing lists, wiki pages, and conference calls set up among accepted attendees. This advance work lays the foundation for participants to be productive from the very first day. This also means that participants should be willing to contribute some time in advance of the hackathon itself to participate in this preparatory discussion. During the Event Typically, hackathon participants use the morning of the first day of the event to organize themselves into working groups of between 3 and 6 people, each with a focused implementation objective. Ideas and objectives are discussed, and attendees coalesce around the projects in which they have the most experience or interest. Deliverables / Event Results The meeting's attendance, working groups, and outcomes will be fully logged and documented on the GMOD wiki (http://gmod.org). Each working group during the event will typically have its own wiki page, linked from the main EvoHack page, where it documents its minutes and design notes, and provides links to the code and documentation it produces. Also, since GMOD and NESCent are both committed to open source principles, all code and documentation produced by participants during the hackathon must be published under an OSI-approved open source license. As contributions to existing GMOD tools, all hackathon products will most likely satisfy this requirement automatically. NESCent This event is sponsored by the US National Evolutionary Synthesis Center (NESCent, http://www.nescent.org) through its Informatics Whitepapers program (http://www.nescent.org/informatics/whitepapers.php). NESCent promotes the synthesis of information, concepts and knowledge to address significant, emerging, or novel questions in evolutionary science and its applications. NESCent achieves this by supporting research and education across disciplinary, institutional, geographic, and demographic boundaries (see http://www.nescent.org/science/proposals.php). Links Main GMOD EvoHack page, and full proposal: http://gmod.org/wiki/GMOD_Evo_Hackathon NESCent: http://www.nescent.org/ GMOD: http://gmod.org Similar past NESCent events, see: http://hackathon.nescent.org/ GMOD hackathon application: http://bit.ly/gmodevohack -- http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/GMOD_Europe_2010 http://gmod.org/wiki/Help_Desk_Feedback From cjfields at illinois.edu Fri Aug 6 12:28:14 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 6 Aug 2010 11:28:14 -0500 Subject: [Open-bio-l] Open Bio Wiki spamming Message-ID: <9B931D9D-2445-4464-80B3-3882A6B75188@illinois.edu> All, I found a ton of spammed links on the main OBF wiki this morning, spanning the last month. My guess is this has been going on for a bit now (e.g. beyond the last month). Anyone know of a way to check over edits past one month? Also wondering if we need to go with a better captcha system than what we currently have in place. Any suggestions? chris From andy.jenkinson at ebi.ac.uk Fri Aug 6 13:44:38 2010 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Fri, 6 Aug 2010 18:44:38 +0100 Subject: [Open-bio-l] Open Bio Wiki spamming In-Reply-To: <9B931D9D-2445-4464-80B3-3882A6B75188@illinois.edu> References: <9B931D9D-2445-4464-80B3-3882A6B75188@illinois.edu> Message-ID: The biodas wiki has tons, but not all visible - mostly user pages. I gave up doing anything about it unless I spot it on a page. You can do: http://www.biodas.org/w/index.php?title=Special:RecentChanges&days=30 I'm not sure if the registrations are automated or not, but I suspect so. A better captcha would be very much appreciated. Cheers, Andy On 6 Aug 2010, at 17:28, Chris Fields wrote: > All, > > I found a ton of spammed links on the main OBF wiki this morning, spanning the last month. My guess is this has been going on for a bit now (e.g. beyond the last month). Anyone know of a way to check over edits past one month? > > Also wondering if we need to go with a better captcha system than what we currently have in place. Any suggestions? > > chris > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l On 6 Aug 2010, at 17:28, Chris Fields wrote: > All, > > I found a ton of spammed links on the main OBF wiki this morning, spanning the last month. My guess is this has been going on for a bit now (e.g. beyond the last month). Anyone know of a way to check over edits past one month? > > Also wondering if we need to go with a better captcha system than what we currently have in place. Any suggestions? > > chris > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l From clements at nescent.org Fri Aug 6 19:08:35 2010 From: clements at nescent.org (Dave Clements) Date: Fri, 6 Aug 2010 16:08:35 -0700 Subject: [Open-bio-l] Open Bio Wiki spamming In-Reply-To: References: <9B931D9D-2445-4464-80B3-3882A6B75188@illinois.edu> Message-ID: Hi Chris, Try http://www.open-bio.org/w/index.php?title=Special:Log&limit=500&month=&year= Dave C On Fri, Aug 6, 2010 at 10:44 AM, Andy Jenkinson wrote: > The biodas wiki has tons, but not all visible - mostly user pages. I gave > up doing anything about it unless I spot it on a page. You can do: > http://www.biodas.org/w/index.php?title=Special:RecentChanges&days=30 > > I'm not sure if the registrations are automated or not, but I suspect so. A > better captcha would be very much appreciated. > > Cheers, > Andy > > On 6 Aug 2010, at 17:28, Chris Fields wrote: > > > All, > > > > I found a ton of spammed links on the main OBF wiki this morning, > spanning the last month. My guess is this has been going on for a bit now > (e.g. beyond the last month). Anyone know of a way to check over edits past > one month? > > > > Also wondering if we need to go with a better captcha system than what we > currently have in place. Any suggestions? > > > > chris > > _______________________________________________ > > Open-Bio-l mailing list > > Open-Bio-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/open-bio-l > > On 6 Aug 2010, at 17:28, Chris Fields wrote: > > > All, > > > > I found a ton of spammed links on the main OBF wiki this morning, > spanning the last month. My guess is this has been going on for a bit now > (e.g. beyond the last month). Anyone know of a way to check over edits past > one month? > > > > Also wondering if we need to go with a better captcha system than what we > currently have in place. Any suggestions? > > > > chris > > _______________________________________________ > > Open-Bio-l mailing list > > Open-Bio-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/open-bio-l > > > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l > -- http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/GMOD_Europe_2010 http://gmod.org/wiki/GMOD_Evo_Hackathon http://gmod.org/wiki/Help_Desk_Feedback From cjfields at illinois.edu Sat Aug 7 01:22:22 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 7 Aug 2010 00:22:22 -0500 Subject: [Open-bio-l] Open Bio Wiki spamming In-Reply-To: References: <9B931D9D-2445-4464-80B3-3882A6B75188@illinois.edu> Message-ID: Thanks Dave. Looks like it's clean pretty much to last August, so I'll not worry about it, beyond re-echoing the need for a better captcha system. chris On Aug 6, 2010, at 6:08 PM, Dave Clements wrote: > Hi Chris, > > Try > > http://www.open-bio.org/w/index.php?title=Special:Log&limit=500&month=&year= > > Dave C > > On Fri, Aug 6, 2010 at 10:44 AM, Andy Jenkinson wrote: > The biodas wiki has tons, but not all visible - mostly user pages. I gave up doing anything about it unless I spot it on a page. You can do: > http://www.biodas.org/w/index.php?title=Special:RecentChanges&days=30 > > I'm not sure if the registrations are automated or not, but I suspect so. A better captcha would be very much appreciated. > > Cheers, > Andy > > On 6 Aug 2010, at 17:28, Chris Fields wrote: > > > All, > > > > I found a ton of spammed links on the main OBF wiki this morning, spanning the last month. My guess is this has been going on for a bit now (e.g. beyond the last month). Anyone know of a way to check over edits past one month? > > > > Also wondering if we need to go with a better captcha system than what we currently have in place. Any suggestions? > > > > chris > > _______________________________________________ > > Open-Bio-l mailing list > > Open-Bio-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/open-bio-l > > On 6 Aug 2010, at 17:28, Chris Fields wrote: > > > All, > > > > I found a ton of spammed links on the main OBF wiki this morning, spanning the last month. My guess is this has been going on for a bit now (e.g. beyond the last month). Anyone know of a way to check over edits past one month? > > > > Also wondering if we need to go with a better captcha system than what we currently have in place. Any suggestions? > > > > chris > > _______________________________________________ > > Open-Bio-l mailing list > > Open-Bio-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/open-bio-l > > > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l > > > > -- > http://gmod.org/wiki/GMOD_News > http://gmod.org/wiki/GMOD_Europe_2010 > http://gmod.org/wiki/GMOD_Evo_Hackathon > http://gmod.org/wiki/Help_Desk_Feedback From David.Messina at sbc.su.se Sat Aug 7 02:07:40 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Sat, 7 Aug 2010 08:07:40 +0200 Subject: [Open-bio-l] Open Bio Wiki spamming In-Reply-To: References: <9B931D9D-2445-4464-80B3-3882A6B75188@illinois.edu> Message-ID: Is it possible to tell whether the spam account was created by machine and not human? If a human, better captcha might not help us. Dave From dan.bolser at gmail.com Mon Aug 9 04:22:55 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 9 Aug 2010 09:22:55 +0100 Subject: [Open-bio-l] Open Bio Wiki spamming In-Reply-To: References: <9B931D9D-2445-4464-80B3-3882A6B75188@illinois.edu> Message-ID: This captcha plugin (and rule set) has never let me down: http://www.mediawiki.org/wiki/Extension:ReCAPTCHA If you have the 'AskSQL' extension installed [1], you can directly query the database in order to detect spamming accounts (see below). I then typically list all the edits by those users and revert them all before deleting the user [2]. Another strategy is to merge all spammers into one user and do a mass 'rollback'. [1] http://www.mediawiki.org/wiki/Asksql [2] http://www.mediawiki.org/wiki/Extension:User_Merge_and_Delete There are also other dedicated spam cleanup extensions, but I never found a 'killer-app' for this job. Here is a couple of queries that may help: * Funnily enough, many of the spam accounts use the same email address: SELECT RIGHT(user_email, LENGTH(user_email) - LOCATE("@", user_email)) AS mail_domain, COUNT(*) AS domain_count FROM prefix_user GROUP BY mail_domain HAVING domain_count > 1 ; * Your top editors may well be spammers... SELECT * FROM ( SELECT rev_user_text, COUNT(*) AS EDITS FROM prefix_revision GROUP BY rev_user_text ) AS inner_table ORDER BY EDITS DESC LIMIT 20 ; HTH, Dan. P.S. Since we're talking spam ;-) NETTAB 2010 workshop focused on: Biological Wikis! November 29 - December 1, 2010, Naples, Italy http://www.nettab.org/2010/ On 7 August 2010 07:07, Dave Messina wrote: > Is it possible to tell whether the spam account was created by machine and not human? > > If a human, better captcha might not help us. > > > Dave > > > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l > From p.j.a.cock at googlemail.com Tue Aug 10 11:24:07 2010 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 10 Aug 2010 16:24:07 +0100 Subject: [Open-bio-l] Open Bio Wiki spamming In-Reply-To: References: <9B931D9D-2445-4464-80B3-3882A6B75188@illinois.edu> Message-ID: On Fri, Aug 6, 2010 at 6:44 PM, Andy Jenkinson wrote: > The biodas wiki has tons, but not all visible - mostly user pages. I gave up doin > anything about it unless I spot it on a page. You can do: > http://www.biodas.org/w/index.php?title=Special:RecentChanges&days=30 > > I'm not sure if the registrations are automated or not, but I suspect so. A better > captcha would be very much appreciated. > > Cheers, > Andy Same here on the Biopython wiki: I've just reverted one spam page from the weekend which was probably a human vandal (single user account). Subscribing to the RSS feed of wiki changes is a good way to stay on top of this. See also this ticket from May 2010, where from the volume of accounts it did look automated: [O|B|F Helpdesk #923] AutoReply: 100s of spam accounts created on Biopython wiki Peter From rmb32 at cornell.edu Thu Aug 19 13:09:45 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Thu, 19 Aug 2010 10:09:45 -0700 Subject: [Open-bio-l] reminder: Aug 25 deadline for GMOD Hackathon application Message-ID: <4C6D6559.3080809@cornell.edu> Hi all, This is your one-week reminder: the deadline for open applications to the GMOD Evo hackathon is Wednesday, August 25th. Rob ======================================== We are seeking participants for the GMOD Tools for Evolutionary Biology Hackathon, held November 8-12, 2010 at the US National Evolutionary Synthesis Center (NESCent) in Durham, NC. This hackathon targets three critical gaps in the capabilities of the GMOD toolbox that currently limit its utility for evolutionary research: 1. Visualization of comparative genomics data 2. Visualization of phylogenetic data and trees 3. Support for population diversity and phenotype data If you are interested in these areas and have relevant expertise, you are strongly encouraged to apply. Relevant areas of expertise include more than just software development: if you are a GMOD power user, visualization guru, domain expert (comparative, phylogenetics, population, ...), or documentation wizard, then your skills are needed! How To Apply: Fill out the online application form at http://bit.ly/gmodevohack. Applications are due August 25. About GMOD: GMOD is an intercompatible suite of open-source software components for storing, managing, analyzing, and visualizing genome-scale data. GMOD includes many widely-used software components: GBrowse and JBrowse, both genome viewers; GBrowse_syn, a comparative genomics viewer; Chado, a generic and modular database schema; CMap, a comparative map viewer; as well as many other components including Apollo, MAKER, BioMart, InterMine, and Galaxy. We hope to extend the functionality of existing GMOD components, and integrate new components as well. About Hackathons: A hackathon is an intense event at which a group of programmers with different backgrounds and skills collaborate hands-on and face-to-face to develop working code that is of utility to the community as a whole. The mix of people will include domain experts and computer-savvy end-users. More details about the event, its motivation, organization, procedures, and attendees, as well as URLs to the hackathon and related websites are included below. Sincerely, The GMOD EvoHack Organizing Committee (and project affiliations as relevant): Nicole Washington, Chair (LBNL, modENCODE, Phenote) Robert Buels (SGN, Chado NatDiv) Scott Cain (OICR, GMOD) Dave Clements (NESCent, GMOD) Hilmar Lapp (NESCent, Phenoscape, Chado NatDiv) Sheldon McKay (University of Arizona, iPlant, GBrowse_syn) ----------------------------- About the GMOD Evo Hackathon Overview We are organizing a hackathon to fill critical gaps in the capabilities of the Generic Model Organism Database (GMOD) toolbox that currently limit its utility for evolutionary research. Specifically, we will focus on tools for 1) viewing comparative genomics data; 2) visualizing phylogenomic data; and 3) supporting population diversity data and phenotype annotation. The event will be hosted at NESCent and bring together a group of about 20+ software developers, end-user representatives, and documentation experts who would otherwise not meet. The participants will include key developers of GMOD components that currently lack features critical for emerging evolutionary biology research, developers of informatics tools in evolutionary research that lack GMOD integration, and informatics-savvy biologists who can represent end-user requirements. The event will provide a unique opportunity to infuse the GMOD developer community with a heightened awareness of unmet needs in evolutionary biology that GMOD components have the potential to fill, and for tool developers in evolutionary biology to better understand how best to extend or integrate with already existing GMOD components. Before the Event Discussion of ideas and sometimes even design actually starts well before the hackathon, on mailing lists, wiki pages, and conference calls set up among accepted attendees. This advance work lays the foundation for participants to be productive from the very first day. This also means that participants should be willing to contribute some time in advance of the hackathon itself to participate in this preparatory discussion. During the Event Typically, hackathon participants use the morning of the first day of the event to organize themselves into working groups of between 3 and 6 people, each with a focused implementation objective. Ideas and objectives are discussed, and attendees coalesce around the projects in which they have the most experience or interest. Deliverables / Event Results The meeting's attendance, working groups, and outcomes will be fully logged and documented on the GMOD wiki (http://gmod.org). Each working group during the event will typically have its own wiki page, linked from the main EvoHack page, where it documents its minutes and design notes, and provides links to the code and documentation it produces. Also, since GMOD and NESCent are both committed to open source principles, all code and documentation produced by participants during the hackathon must be published under an OSI-approved open source license. As contributions to existing GMOD tools, all hackathon products will most likely satisfy this requirement automatically. NESCent This event is sponsored by the US National Evolutionary Synthesis Center (NESCent, http://www.nescent.org) through its Informatics Whitepapers program (http://www.nescent.org/informatics/whitepapers.php). NESCent promotes the synthesis of information, concepts and knowledge to address significant, emerging, or novel questions in evolutionary science and its applications. NESCent achieves this by supporting research and education across disciplinary, institutional, geographic, and demographic boundaries (see http://www.nescent.org/science/proposals.php). Links Main GMOD EvoHack page, and full proposal: http://gmod.org/wiki/GMOD_Evo_Hackathon NESCent: http://www.nescent.org/ GMOD: http://gmod.org Similar past NESCent events, see: http://hackathon.nescent.org/ GMOD hackathon application: http://bit.ly/gmodevohack -- http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/GMOD_Europe_2010 http://gmod.org/wiki/Help_Desk_Feedback From biopython at maubp.freeserve.co.uk Thu Aug 26 06:57:27 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 26 Aug 2010 11:57:27 +0100 Subject: [Open-bio-l] Problem with biopython.org domain Message-ID: Hi all, We appear to have a temporary problem with our biopython.org domain, which I trust the OBF admin team will address shortly. As a fallback you can use http://biopython.open-bio.org/wiki/Main_Page and http://biopython.open-bio.org/DIST/ for the downloads. Source code is hosted separately on github, http://github.com/biopython/biopython/ Apologies, Peter From dag at sonsorol.org Thu Aug 26 07:26:57 2010 From: dag at sonsorol.org (Chris Dagdigian) Date: Thu, 26 Aug 2010 07:26:57 -0400 Subject: [Open-bio-l] Problem with biopython.org domain In-Reply-To: References: Message-ID: <4C764F81.1060100@sonsorol.org> I manage or am the admin/technical/billing account holder for 24 domains, among them most of the open-bio.org ones. Biopython.org is one that I do not own. Actually since NetSol is offering to let me change DNS maybe I'm the technical contact - have to wait and see on this. Normally for domains I control netsol starts email nagging me constantly - never got emails about this one. However, Networksolutions allows *anyone* with a payment method to renew any domain for any reason. I've renewed biopython.org for a 2-year term, paying out of pocket like I do for all OBF domains so our $$ stays in our bank account. > Order Confirmation > > Order Number: 375229424 > Today's Charges: $65.98 > Future Charges: $0.00 > Credit Card: xxxxxxxxxxx1002 The site should be back up soonish. I can't change the DNS entry that points the website to the expired splash page until netsol processes the renewal. Upcoming domain expiration dates: biomoby.org will expire Oct 1 bior.org will expire Nov 5 biosoap.org will expire Oct 9 -Chris Peter wrote: > Hi all, > > We appear to have a temporary problem with our biopython.org domain, > which I trust the OBF admin team will address shortly. > > As a fallback you can use http://biopython.open-bio.org/wiki/Main_Page > and http://biopython.open-bio.org/DIST/ for the downloads. > > Source code is hosted separately on github, > http://github.com/biopython/biopython/ > > Apologies, > > Peter > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l From biopython at maubp.freeserve.co.uk Thu Aug 26 08:03:48 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 26 Aug 2010 13:03:48 +0100 Subject: [Open-bio-l] [Biopython] Problem with biopython.org domain In-Reply-To: <4C764F81.1060100@sonsorol.org> References: <4C764F81.1060100@sonsorol.org> Message-ID: On Thu, Aug 26, 2010 at 12:26 PM, Chris Dagdigian wrote: > > I manage or am the admin/technical/billing account holder for 24 domains, > among them most of the open-bio.org ones. > > Biopython.org is one that I do not own. Actually since NetSol is offering to > let me change DNS maybe I'm the technical contact - have to wait and see on > this. Normally for domains I control netsol starts email nagging me > constantly - never got emails about this one. > > > However, Networksolutions allows *anyone* with a payment method to renew any > domain for any reason. > > I've renewed biopython.org for a 2-year term, paying out of pocket like I do > for all OBF domains so our $$ stays in our bank account. > > >> Order Confirmation >> >> Order Number: 375229424 >> Today's Charges: $65.98 >> Future Charges: $0.00 >> Credit Card: xxxxxxxxxxx1002 > > The site should be back up soonish. I can't change the DNS entry that points > the website to the expired splash page until netsol processes the renewal. > > Upcoming domain expiration dates: > > biomoby.org will expire Oct 1 > bior.org will expire Nov 5 > biosoap.org will expire Oct 9 > > > -Chris Thanks Chris :) Will you be able to update the domain's contact details to be consistent with the other Bio* domains? Peter From biopython at maubp.freeserve.co.uk Fri Aug 27 04:57:04 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Fri, 27 Aug 2010 09:57:04 +0100 Subject: [Open-bio-l] [Biopython] Problem with biopython.org domain In-Reply-To: <4C764F81.1060100@sonsorol.org> References: <4C764F81.1060100@sonsorol.org> Message-ID: On Thu, Aug 26, 2010 at 12:26 PM, Chris Dagdigian wrote: > > I manage or am the admin/technical/billing account holder for 24 > domains, among them most of the open-bio.org ones. ... I've > renewed biopython.org for a 2-year term, ... The site should be > back up soonish. Thanks for the speedy response Chris - www.biopython.org is back up now. If anyone is still having trouble, please allow another day or so for DNS servers to update. As a fallback you can use http://biopython.open-bio.org/wiki/Main_Page and http://biopython.open-bio.org/DIST/ for the downloads. Source code is hosted separately on github, http://github.com/biopython/biopython/ Peter From rmb32 at cornell.edu Sun Aug 1 19:17:14 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Sun, 01 Aug 2010 12:17:14 -0700 Subject: [Open-bio-l] GMOD Evo Hackathon Open Call for Participation Message-ID: <4C55C83A.3060700@cornell.edu> We are seeking participants for the GMOD Tools for Evolutionary Biology Hackathon, held November 8-12, 2010 at the US National Evolutionary Synthesis Center (NESCent) in Durham, NC. This hackathon targets three critical gaps in the capabilities of the GMOD toolbox that currently limit its utility for evolutionary research: 1. Visualization of comparative genomics data 2. Visualization of phylogenetic data and trees 3. Support for population diversity and phenotype data If you are interested in these areas and have relevant expertise, you are strongly encouraged to apply. Relevant areas of expertise include more than just software development: if you are a GMOD power user, visualization guru, domain expert (comparative, phylogenetics, population, ...), or documentation wizard, then your skills are needed! How To Apply: Fill out the online application form at http://bit.ly/gmodevohack. Applications are due August 25. About GMOD: GMOD is an intercompatible suite of open-source software components for storing, managing, analyzing, and visualizing genome-scale data. GMOD includes many widely-used software components: GBrowse and JBrowse, both genome viewers; GBrowse_syn, a comparative genomics viewer; Chado, a generic and modular database schema; CMap, a comparative map viewer; as well as many other components including Apollo, MAKER, BioMart, InterMine, and Galaxy. We hope to extend the functionality of existing GMOD components, and integrate new components as well. About Hackathons: A hackathon is an intense event at which a group of programmers with different backgrounds and skills collaborate hands-on and face-to-face to develop working code that is of utility to the community as a whole. The mix of people will include domain experts and computer-savvy end-users. More details about the event, its motivation, organization, procedures, and attendees, as well as URLs to the hackathon and related websites are included below. Sincerely, The GMOD EvoHack Organizing Committee (and project affiliations as relevant): Nicole Washington, Chair (LBNL, modENCODE, Phenote) Robert Buels (SGN, Chado NatDiv) Scott Cain (OICR, GMOD) Dave Clements (NESCent, GMOD) Hilmar Lapp (NESCent, Phenoscape, Chado NatDiv) Sheldon McKay (University of Arizona, iPlant, GBrowse_syn) ----------------------------- About the GMOD Evo Hackathon Overview We are organizing a hackathon to fill critical gaps in the capabilities of the Generic Model Organism Database (GMOD) toolbox that currently limit its utility for evolutionary research. Specifically, we will focus on tools for 1) viewing comparative genomics data; 2) visualizing phylogenomic data; and 3) supporting population diversity data and phenotype annotation. The event will be hosted at NESCent and bring together a group of about 20+ software developers, end-user representatives, and documentation experts who would otherwise not meet. The participants will include key developers of GMOD components that currently lack features critical for emerging evolutionary biology research, developers of informatics tools in evolutionary research that lack GMOD integration, and informatics-savvy biologists who can represent end-user requirements. The event will provide a unique opportunity to infuse the GMOD developer community with a heightened awareness of unmet needs in evolutionary biology that GMOD components have the potential to fill, and for tool developers in evolutionary biology to better understand how best to extend or integrate with already existing GMOD components. Before the Event Discussion of ideas and sometimes even design actually starts well before the hackathon, on mailing lists, wiki pages, and conference calls set up among accepted attendees. This advance work lays the foundation for participants to be productive from the very first day. This also means that participants should be willing to contribute some time in advance of the hackathon itself to participate in this preparatory discussion. During the Event Typically, hackathon participants use the morning of the first day of the event to organize themselves into working groups of between 3 and 6 people, each with a focused implementation objective. Ideas and objectives are discussed, and attendees coalesce around the projects in which they have the most experience or interest. Deliverables / Event Results The meeting's attendance, working groups, and outcomes will be fully logged and documented on the GMOD wiki (http://gmod.org). Each working group during the event will typically have its own wiki page, linked from the main EvoHack page, where it documents its minutes and design notes, and provides links to the code and documentation it produces. Also, since GMOD and NESCent are both committed to open source principles, all code and documentation produced by participants during the hackathon must be published under an OSI-approved open source license. As contributions to existing GMOD tools, all hackathon products will most likely satisfy this requirement automatically. NESCent This event is sponsored by the US National Evolutionary Synthesis Center (NESCent, http://www.nescent.org) through its Informatics Whitepapers program (http://www.nescent.org/informatics/whitepapers.php). NESCent promotes the synthesis of information, concepts and knowledge to address significant, emerging, or novel questions in evolutionary science and its applications. NESCent achieves this by supporting research and education across disciplinary, institutional, geographic, and demographic boundaries (see http://www.nescent.org/science/proposals.php). Links Main GMOD EvoHack page, and full proposal: http://gmod.org/wiki/GMOD_Evo_Hackathon NESCent: http://www.nescent.org/ GMOD: http://gmod.org Similar past NESCent events, see: http://hackathon.nescent.org/ GMOD hackathon application: http://bit.ly/gmodevohack -- http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/GMOD_Europe_2010 http://gmod.org/wiki/Help_Desk_Feedback From cjfields at illinois.edu Fri Aug 6 16:28:14 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 6 Aug 2010 11:28:14 -0500 Subject: [Open-bio-l] Open Bio Wiki spamming Message-ID: <9B931D9D-2445-4464-80B3-3882A6B75188@illinois.edu> All, I found a ton of spammed links on the main OBF wiki this morning, spanning the last month. My guess is this has been going on for a bit now (e.g. beyond the last month). Anyone know of a way to check over edits past one month? Also wondering if we need to go with a better captcha system than what we currently have in place. Any suggestions? chris From andy.jenkinson at ebi.ac.uk Fri Aug 6 17:44:38 2010 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Fri, 6 Aug 2010 18:44:38 +0100 Subject: [Open-bio-l] Open Bio Wiki spamming In-Reply-To: <9B931D9D-2445-4464-80B3-3882A6B75188@illinois.edu> References: <9B931D9D-2445-4464-80B3-3882A6B75188@illinois.edu> Message-ID: The biodas wiki has tons, but not all visible - mostly user pages. I gave up doing anything about it unless I spot it on a page. You can do: http://www.biodas.org/w/index.php?title=Special:RecentChanges&days=30 I'm not sure if the registrations are automated or not, but I suspect so. A better captcha would be very much appreciated. Cheers, Andy On 6 Aug 2010, at 17:28, Chris Fields wrote: > All, > > I found a ton of spammed links on the main OBF wiki this morning, spanning the last month. My guess is this has been going on for a bit now (e.g. beyond the last month). Anyone know of a way to check over edits past one month? > > Also wondering if we need to go with a better captcha system than what we currently have in place. Any suggestions? > > chris > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l On 6 Aug 2010, at 17:28, Chris Fields wrote: > All, > > I found a ton of spammed links on the main OBF wiki this morning, spanning the last month. My guess is this has been going on for a bit now (e.g. beyond the last month). Anyone know of a way to check over edits past one month? > > Also wondering if we need to go with a better captcha system than what we currently have in place. Any suggestions? > > chris > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l From clements at nescent.org Fri Aug 6 23:08:35 2010 From: clements at nescent.org (Dave Clements) Date: Fri, 6 Aug 2010 16:08:35 -0700 Subject: [Open-bio-l] Open Bio Wiki spamming In-Reply-To: References: <9B931D9D-2445-4464-80B3-3882A6B75188@illinois.edu> Message-ID: Hi Chris, Try http://www.open-bio.org/w/index.php?title=Special:Log&limit=500&month=&year= Dave C On Fri, Aug 6, 2010 at 10:44 AM, Andy Jenkinson wrote: > The biodas wiki has tons, but not all visible - mostly user pages. I gave > up doing anything about it unless I spot it on a page. You can do: > http://www.biodas.org/w/index.php?title=Special:RecentChanges&days=30 > > I'm not sure if the registrations are automated or not, but I suspect so. A > better captcha would be very much appreciated. > > Cheers, > Andy > > On 6 Aug 2010, at 17:28, Chris Fields wrote: > > > All, > > > > I found a ton of spammed links on the main OBF wiki this morning, > spanning the last month. My guess is this has been going on for a bit now > (e.g. beyond the last month). Anyone know of a way to check over edits past > one month? > > > > Also wondering if we need to go with a better captcha system than what we > currently have in place. Any suggestions? > > > > chris > > _______________________________________________ > > Open-Bio-l mailing list > > Open-Bio-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/open-bio-l > > On 6 Aug 2010, at 17:28, Chris Fields wrote: > > > All, > > > > I found a ton of spammed links on the main OBF wiki this morning, > spanning the last month. My guess is this has been going on for a bit now > (e.g. beyond the last month). Anyone know of a way to check over edits past > one month? > > > > Also wondering if we need to go with a better captcha system than what we > currently have in place. Any suggestions? > > > > chris > > _______________________________________________ > > Open-Bio-l mailing list > > Open-Bio-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/open-bio-l > > > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l > -- http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/GMOD_Europe_2010 http://gmod.org/wiki/GMOD_Evo_Hackathon http://gmod.org/wiki/Help_Desk_Feedback From cjfields at illinois.edu Sat Aug 7 05:22:22 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 7 Aug 2010 00:22:22 -0500 Subject: [Open-bio-l] Open Bio Wiki spamming In-Reply-To: References: <9B931D9D-2445-4464-80B3-3882A6B75188@illinois.edu> Message-ID: Thanks Dave. Looks like it's clean pretty much to last August, so I'll not worry about it, beyond re-echoing the need for a better captcha system. chris On Aug 6, 2010, at 6:08 PM, Dave Clements wrote: > Hi Chris, > > Try > > http://www.open-bio.org/w/index.php?title=Special:Log&limit=500&month=&year= > > Dave C > > On Fri, Aug 6, 2010 at 10:44 AM, Andy Jenkinson wrote: > The biodas wiki has tons, but not all visible - mostly user pages. I gave up doing anything about it unless I spot it on a page. You can do: > http://www.biodas.org/w/index.php?title=Special:RecentChanges&days=30 > > I'm not sure if the registrations are automated or not, but I suspect so. A better captcha would be very much appreciated. > > Cheers, > Andy > > On 6 Aug 2010, at 17:28, Chris Fields wrote: > > > All, > > > > I found a ton of spammed links on the main OBF wiki this morning, spanning the last month. My guess is this has been going on for a bit now (e.g. beyond the last month). Anyone know of a way to check over edits past one month? > > > > Also wondering if we need to go with a better captcha system than what we currently have in place. Any suggestions? > > > > chris > > _______________________________________________ > > Open-Bio-l mailing list > > Open-Bio-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/open-bio-l > > On 6 Aug 2010, at 17:28, Chris Fields wrote: > > > All, > > > > I found a ton of spammed links on the main OBF wiki this morning, spanning the last month. My guess is this has been going on for a bit now (e.g. beyond the last month). Anyone know of a way to check over edits past one month? > > > > Also wondering if we need to go with a better captcha system than what we currently have in place. Any suggestions? > > > > chris > > _______________________________________________ > > Open-Bio-l mailing list > > Open-Bio-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/open-bio-l > > > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l > > > > -- > http://gmod.org/wiki/GMOD_News > http://gmod.org/wiki/GMOD_Europe_2010 > http://gmod.org/wiki/GMOD_Evo_Hackathon > http://gmod.org/wiki/Help_Desk_Feedback From David.Messina at sbc.su.se Sat Aug 7 06:07:40 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Sat, 7 Aug 2010 08:07:40 +0200 Subject: [Open-bio-l] Open Bio Wiki spamming In-Reply-To: References: <9B931D9D-2445-4464-80B3-3882A6B75188@illinois.edu> Message-ID: Is it possible to tell whether the spam account was created by machine and not human? If a human, better captcha might not help us. Dave From dan.bolser at gmail.com Mon Aug 9 08:22:55 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 9 Aug 2010 09:22:55 +0100 Subject: [Open-bio-l] Open Bio Wiki spamming In-Reply-To: References: <9B931D9D-2445-4464-80B3-3882A6B75188@illinois.edu> Message-ID: This captcha plugin (and rule set) has never let me down: http://www.mediawiki.org/wiki/Extension:ReCAPTCHA If you have the 'AskSQL' extension installed [1], you can directly query the database in order to detect spamming accounts (see below). I then typically list all the edits by those users and revert them all before deleting the user [2]. Another strategy is to merge all spammers into one user and do a mass 'rollback'. [1] http://www.mediawiki.org/wiki/Asksql [2] http://www.mediawiki.org/wiki/Extension:User_Merge_and_Delete There are also other dedicated spam cleanup extensions, but I never found a 'killer-app' for this job. Here is a couple of queries that may help: * Funnily enough, many of the spam accounts use the same email address: SELECT RIGHT(user_email, LENGTH(user_email) - LOCATE("@", user_email)) AS mail_domain, COUNT(*) AS domain_count FROM prefix_user GROUP BY mail_domain HAVING domain_count > 1 ; * Your top editors may well be spammers... SELECT * FROM ( SELECT rev_user_text, COUNT(*) AS EDITS FROM prefix_revision GROUP BY rev_user_text ) AS inner_table ORDER BY EDITS DESC LIMIT 20 ; HTH, Dan. P.S. Since we're talking spam ;-) NETTAB 2010 workshop focused on: Biological Wikis! November 29 - December 1, 2010, Naples, Italy http://www.nettab.org/2010/ On 7 August 2010 07:07, Dave Messina wrote: > Is it possible to tell whether the spam account was created by machine and not human? > > If a human, better captcha might not help us. > > > Dave > > > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l > From p.j.a.cock at googlemail.com Tue Aug 10 15:24:07 2010 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 10 Aug 2010 16:24:07 +0100 Subject: [Open-bio-l] Open Bio Wiki spamming In-Reply-To: References: <9B931D9D-2445-4464-80B3-3882A6B75188@illinois.edu> Message-ID: On Fri, Aug 6, 2010 at 6:44 PM, Andy Jenkinson wrote: > The biodas wiki has tons, but not all visible - mostly user pages. I gave up doin > anything about it unless I spot it on a page. You can do: > http://www.biodas.org/w/index.php?title=Special:RecentChanges&days=30 > > I'm not sure if the registrations are automated or not, but I suspect so. A better > captcha would be very much appreciated. > > Cheers, > Andy Same here on the Biopython wiki: I've just reverted one spam page from the weekend which was probably a human vandal (single user account). Subscribing to the RSS feed of wiki changes is a good way to stay on top of this. See also this ticket from May 2010, where from the volume of accounts it did look automated: [O|B|F Helpdesk #923] AutoReply: 100s of spam accounts created on Biopython wiki Peter From rmb32 at cornell.edu Thu Aug 19 17:09:45 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Thu, 19 Aug 2010 10:09:45 -0700 Subject: [Open-bio-l] reminder: Aug 25 deadline for GMOD Hackathon application Message-ID: <4C6D6559.3080809@cornell.edu> Hi all, This is your one-week reminder: the deadline for open applications to the GMOD Evo hackathon is Wednesday, August 25th. Rob ======================================== We are seeking participants for the GMOD Tools for Evolutionary Biology Hackathon, held November 8-12, 2010 at the US National Evolutionary Synthesis Center (NESCent) in Durham, NC. This hackathon targets three critical gaps in the capabilities of the GMOD toolbox that currently limit its utility for evolutionary research: 1. Visualization of comparative genomics data 2. Visualization of phylogenetic data and trees 3. Support for population diversity and phenotype data If you are interested in these areas and have relevant expertise, you are strongly encouraged to apply. Relevant areas of expertise include more than just software development: if you are a GMOD power user, visualization guru, domain expert (comparative, phylogenetics, population, ...), or documentation wizard, then your skills are needed! How To Apply: Fill out the online application form at http://bit.ly/gmodevohack. Applications are due August 25. About GMOD: GMOD is an intercompatible suite of open-source software components for storing, managing, analyzing, and visualizing genome-scale data. GMOD includes many widely-used software components: GBrowse and JBrowse, both genome viewers; GBrowse_syn, a comparative genomics viewer; Chado, a generic and modular database schema; CMap, a comparative map viewer; as well as many other components including Apollo, MAKER, BioMart, InterMine, and Galaxy. We hope to extend the functionality of existing GMOD components, and integrate new components as well. About Hackathons: A hackathon is an intense event at which a group of programmers with different backgrounds and skills collaborate hands-on and face-to-face to develop working code that is of utility to the community as a whole. The mix of people will include domain experts and computer-savvy end-users. More details about the event, its motivation, organization, procedures, and attendees, as well as URLs to the hackathon and related websites are included below. Sincerely, The GMOD EvoHack Organizing Committee (and project affiliations as relevant): Nicole Washington, Chair (LBNL, modENCODE, Phenote) Robert Buels (SGN, Chado NatDiv) Scott Cain (OICR, GMOD) Dave Clements (NESCent, GMOD) Hilmar Lapp (NESCent, Phenoscape, Chado NatDiv) Sheldon McKay (University of Arizona, iPlant, GBrowse_syn) ----------------------------- About the GMOD Evo Hackathon Overview We are organizing a hackathon to fill critical gaps in the capabilities of the Generic Model Organism Database (GMOD) toolbox that currently limit its utility for evolutionary research. Specifically, we will focus on tools for 1) viewing comparative genomics data; 2) visualizing phylogenomic data; and 3) supporting population diversity data and phenotype annotation. The event will be hosted at NESCent and bring together a group of about 20+ software developers, end-user representatives, and documentation experts who would otherwise not meet. The participants will include key developers of GMOD components that currently lack features critical for emerging evolutionary biology research, developers of informatics tools in evolutionary research that lack GMOD integration, and informatics-savvy biologists who can represent end-user requirements. The event will provide a unique opportunity to infuse the GMOD developer community with a heightened awareness of unmet needs in evolutionary biology that GMOD components have the potential to fill, and for tool developers in evolutionary biology to better understand how best to extend or integrate with already existing GMOD components. Before the Event Discussion of ideas and sometimes even design actually starts well before the hackathon, on mailing lists, wiki pages, and conference calls set up among accepted attendees. This advance work lays the foundation for participants to be productive from the very first day. This also means that participants should be willing to contribute some time in advance of the hackathon itself to participate in this preparatory discussion. During the Event Typically, hackathon participants use the morning of the first day of the event to organize themselves into working groups of between 3 and 6 people, each with a focused implementation objective. Ideas and objectives are discussed, and attendees coalesce around the projects in which they have the most experience or interest. Deliverables / Event Results The meeting's attendance, working groups, and outcomes will be fully logged and documented on the GMOD wiki (http://gmod.org). Each working group during the event will typically have its own wiki page, linked from the main EvoHack page, where it documents its minutes and design notes, and provides links to the code and documentation it produces. Also, since GMOD and NESCent are both committed to open source principles, all code and documentation produced by participants during the hackathon must be published under an OSI-approved open source license. As contributions to existing GMOD tools, all hackathon products will most likely satisfy this requirement automatically. NESCent This event is sponsored by the US National Evolutionary Synthesis Center (NESCent, http://www.nescent.org) through its Informatics Whitepapers program (http://www.nescent.org/informatics/whitepapers.php). NESCent promotes the synthesis of information, concepts and knowledge to address significant, emerging, or novel questions in evolutionary science and its applications. NESCent achieves this by supporting research and education across disciplinary, institutional, geographic, and demographic boundaries (see http://www.nescent.org/science/proposals.php). Links Main GMOD EvoHack page, and full proposal: http://gmod.org/wiki/GMOD_Evo_Hackathon NESCent: http://www.nescent.org/ GMOD: http://gmod.org Similar past NESCent events, see: http://hackathon.nescent.org/ GMOD hackathon application: http://bit.ly/gmodevohack -- http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/GMOD_Europe_2010 http://gmod.org/wiki/Help_Desk_Feedback From biopython at maubp.freeserve.co.uk Thu Aug 26 10:57:27 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 26 Aug 2010 11:57:27 +0100 Subject: [Open-bio-l] Problem with biopython.org domain Message-ID: Hi all, We appear to have a temporary problem with our biopython.org domain, which I trust the OBF admin team will address shortly. As a fallback you can use http://biopython.open-bio.org/wiki/Main_Page and http://biopython.open-bio.org/DIST/ for the downloads. Source code is hosted separately on github, http://github.com/biopython/biopython/ Apologies, Peter From dag at sonsorol.org Thu Aug 26 11:26:57 2010 From: dag at sonsorol.org (Chris Dagdigian) Date: Thu, 26 Aug 2010 07:26:57 -0400 Subject: [Open-bio-l] Problem with biopython.org domain In-Reply-To: References: Message-ID: <4C764F81.1060100@sonsorol.org> I manage or am the admin/technical/billing account holder for 24 domains, among them most of the open-bio.org ones. Biopython.org is one that I do not own. Actually since NetSol is offering to let me change DNS maybe I'm the technical contact - have to wait and see on this. Normally for domains I control netsol starts email nagging me constantly - never got emails about this one. However, Networksolutions allows *anyone* with a payment method to renew any domain for any reason. I've renewed biopython.org for a 2-year term, paying out of pocket like I do for all OBF domains so our $$ stays in our bank account. > Order Confirmation > > Order Number: 375229424 > Today's Charges: $65.98 > Future Charges: $0.00 > Credit Card: xxxxxxxxxxx1002 The site should be back up soonish. I can't change the DNS entry that points the website to the expired splash page until netsol processes the renewal. Upcoming domain expiration dates: biomoby.org will expire Oct 1 bior.org will expire Nov 5 biosoap.org will expire Oct 9 -Chris Peter wrote: > Hi all, > > We appear to have a temporary problem with our biopython.org domain, > which I trust the OBF admin team will address shortly. > > As a fallback you can use http://biopython.open-bio.org/wiki/Main_Page > and http://biopython.open-bio.org/DIST/ for the downloads. > > Source code is hosted separately on github, > http://github.com/biopython/biopython/ > > Apologies, > > Peter > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l From biopython at maubp.freeserve.co.uk Thu Aug 26 12:03:48 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 26 Aug 2010 13:03:48 +0100 Subject: [Open-bio-l] [Biopython] Problem with biopython.org domain In-Reply-To: <4C764F81.1060100@sonsorol.org> References: <4C764F81.1060100@sonsorol.org> Message-ID: On Thu, Aug 26, 2010 at 12:26 PM, Chris Dagdigian wrote: > > I manage or am the admin/technical/billing account holder for 24 domains, > among them most of the open-bio.org ones. > > Biopython.org is one that I do not own. Actually since NetSol is offering to > let me change DNS maybe I'm the technical contact - have to wait and see on > this. Normally for domains I control netsol starts email nagging me > constantly - never got emails about this one. > > > However, Networksolutions allows *anyone* with a payment method to renew any > domain for any reason. > > I've renewed biopython.org for a 2-year term, paying out of pocket like I do > for all OBF domains so our $$ stays in our bank account. > > >> Order Confirmation >> >> Order Number: 375229424 >> Today's Charges: $65.98 >> Future Charges: $0.00 >> Credit Card: xxxxxxxxxxx1002 > > The site should be back up soonish. I can't change the DNS entry that points > the website to the expired splash page until netsol processes the renewal. > > Upcoming domain expiration dates: > > biomoby.org will expire Oct 1 > bior.org will expire Nov 5 > biosoap.org will expire Oct 9 > > > -Chris Thanks Chris :) Will you be able to update the domain's contact details to be consistent with the other Bio* domains? Peter From biopython at maubp.freeserve.co.uk Fri Aug 27 08:57:04 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Fri, 27 Aug 2010 09:57:04 +0100 Subject: [Open-bio-l] [Biopython] Problem with biopython.org domain In-Reply-To: <4C764F81.1060100@sonsorol.org> References: <4C764F81.1060100@sonsorol.org> Message-ID: On Thu, Aug 26, 2010 at 12:26 PM, Chris Dagdigian wrote: > > I manage or am the admin/technical/billing account holder for 24 > domains, among them most of the open-bio.org ones. ... I've > renewed biopython.org for a 2-year term, ... The site should be > back up soonish. Thanks for the speedy response Chris - www.biopython.org is back up now. If anyone is still having trouble, please allow another day or so for DNS servers to update. As a fallback you can use http://biopython.open-bio.org/wiki/Main_Page and http://biopython.open-bio.org/DIST/ for the downloads. Source code is hosted separately on github, http://github.com/biopython/biopython/ Peter