Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
Is this conference open for anyone or just (self appointed?) Czars? :) Regards, Thon de Boer, Ph.D. Bioinformatics Guru +1-650-799-6839 thondeb...@me.com LinkedIn Profile On Jun 28, 2012, at 2:14 AM, Sebastian Schaaf wrote: Also hello to everyone, As I browsed through those tabs which are open for weeks I rediscovered the online survey Interested in Deploying Your Own Local Galaxy? connected to this thread here. The last response I could find in this context was the one below which was written by Ann. To make it short: did anything happen in the meantime, has there been any telephone conference, is there still any interest out there? I filled out the survey and ask myself wether it makes still sense to submit the form. Regarding the fact I can participate in this year's Galaxy Developers Conference (GCC in Chicago) I would be quite happy if some contacts may arise from this thread or the conference or both in a mutual way (which would be somewhat perfect). The heavily discussed topic regarding time zones should not prevent us from going ahead. Best regards and thanks in advance, Sebastian Schaaf (Munich, Germany) Ann Black-Ziegelbein schrieb: Hello everyone! Here is a link to a brief survey about how you are using, or plan to use Galaxy locally. If you could take a moment to complete the survey, it will help steer the teleconferences as we get going (and also alleviate having to spend time on the call providing the same background info). The results of the survey will be made public off of a new wiki site that Galaxy's Dave Clements is arranging for the group - thanks Dave! Web Survey: https://docs.google.com/spreadsheet/viewform?formkey=dGJZcmxEWDQ3aERPNmlBaDl1eHVsQ3c6MQ Once the teleconference infrastructure details are in place and finalized, I will send out a web poll to see if we can find a time that works for the majority. Thanks, Ann Black-Ziegelbein On 4/27/2012 2:14 PM, Ryan Golhar wrote: This is a great idea. On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein annbl...@eng.uiowa.edu mailto:annbl...@eng.uiowa.edu wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Sebastian Schaaf, M.Sc. Bioinformatics Chair of Biometry and Bioinformatics Department of Medical Information Sciences, Biometry and Epidemiology University of Munich Marchioninistr. 15, K U1 (postal) Marchioninistr. 17, U 006 (office) D-81377 Munich (Germany) Tel: +49 89 2180-78229 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
For anyone :) Please join us on Monday - Thanks, Ann On 7/5/2012 4:15 PM, Thon Deboer wrote: Is this conference open for anyone or just (self appointed?) Czars? :) Regards, Thon de Boer, Ph.D. Bioinformatics Guru +1-650-799-6839 thondeb...@me.com mailto:thondeb...@me.com LinkedIn Profile http://www.linkedin.com/pub/thon-de-boer/1/1ba/a5b On Jun 28, 2012, at 2:14 AM, Sebastian Schaaf wrote: Also hello to everyone, As I browsed through those tabs which are open for weeks I rediscovered the online survey Interested in Deploying Your Own Local Galaxy? connected to this thread here. The last response I could find in this context was the one below which was written by Ann. To make it short: did anything happen in the meantime, has there been any telephone conference, is there still any interest out there? I filled out the survey and ask myself wether it makes still sense to submit the form. Regarding the fact I can participate in this year's Galaxy Developers Conference (GCC in Chicago) I would be quite happy if some contacts may arise from this thread or the conference or both in a mutual way (which would be somewhat perfect). The heavily discussed topic regarding time zones should not prevent us from going ahead. Best regards and thanks in advance, Sebastian Schaaf (Munich, Germany) Ann Black-Ziegelbein schrieb: Hello everyone! Here is a link to a brief survey about how you are using, or plan to use Galaxy locally. If you could take a moment to complete the survey, it will help steer the teleconferences as we get going (and also alleviate having to spend time on the call providing the same background info). The results of the survey will be made public off of a new wiki site that Galaxy's Dave Clements is arranging for the group - thanks Dave! Web Survey: https://docs.google.com/spreadsheet/viewform?formkey=dGJZcmxEWDQ3aERPNmlBaDl1eHVsQ3c6MQ Once the teleconference infrastructure details are in place and finalized, I will send out a web poll to see if we can find a time that works for the majority. Thanks, Ann Black-Ziegelbein On 4/27/2012 2:14 PM, Ryan Golhar wrote: This is a great idea. On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein annbl...@eng.uiowa.edu mailto:annbl...@eng.uiowa.edu mailto:annbl...@eng.uiowa.edu wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Sebastian Schaaf, M.Sc. Bioinformatics Chair of Biometry and Bioinformatics Department of Medical Information Sciences, Biometry and Epidemiology University of Munich Marchioninistr. 15, K U1 (postal) Marchioninistr. 17, U 006 (office) D-81377 Munich (Germany) Tel: +49 89 2180-78229 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
Also hello to everyone, As I browsed through those tabs which are open for weeks I rediscovered the online survey Interested in Deploying Your Own Local Galaxy? connected to this thread here. The last response I could find in this context was the one below which was written by Ann. To make it short: did anything happen in the meantime, has there been any telephone conference, is there still any interest out there? I filled out the survey and ask myself wether it makes still sense to submit the form. Regarding the fact I can participate in this year's Galaxy Developers Conference (GCC in Chicago) I would be quite happy if some contacts may arise from this thread or the conference or both in a mutual way (which would be somewhat perfect). The heavily discussed topic regarding time zones should not prevent us from going ahead. Best regards and thanks in advance, Sebastian Schaaf (Munich, Germany) Ann Black-Ziegelbein schrieb: Hello everyone! Here is a link to a brief survey about how you are using, or plan to use Galaxy locally. If you could take a moment to complete the survey, it will help steer the teleconferences as we get going (and also alleviate having to spend time on the call providing the same background info). The results of the survey will be made public off of a new wiki site that Galaxy's Dave Clements is arranging for the group - thanks Dave! Web Survey: https://docs.google.com/spreadsheet/viewform?formkey=dGJZcmxEWDQ3aERPNmlBaDl1eHVsQ3c6MQ Once the teleconference infrastructure details are in place and finalized, I will send out a web poll to see if we can find a time that works for the majority. Thanks, Ann Black-Ziegelbein On 4/27/2012 2:14 PM, Ryan Golhar wrote: This is a great idea. On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein annbl...@eng.uiowa.edu mailto:annbl...@eng.uiowa.edu wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Sebastian Schaaf, M.Sc. Bioinformatics Chair of Biometry and Bioinformatics Department of Medical Information Sciences, Biometry and Epidemiology University of Munich Marchioninistr. 15, K U1 (postal) Marchioninistr. 17, U 006 (office) D-81377 Munich (Germany) Tel: +49 89 2180-78229 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
Hi All - I have dropped the ball on this one. We at Iowa have gotten bogged down in storage issues with galaxy (our existing storage was crashing) and have been spending all my time evaluating different storage solutions under load: zfs, gluster, lustre, nfs for our galaxy and high performance compute cluster. This week our testing and evaluation is almost completed. I have a proposed agenda for our first call I need to circulate as well I have lined up an online web conference solution for us to try which will allow our calls to be recorded and posted for playback. I am actually talking to Dave today and hopefully I will get something out for a call in early to mid July. Sorry folks, I have been busy and it has been hard to get back to this. Ann On 6/28/2012 4:14 AM, Sebastian Schaaf wrote: Also hello to everyone, As I browsed through those tabs which are open for weeks I rediscovered the online survey Interested in Deploying Your Own Local Galaxy? connected to this thread here. The last response I could find in this context was the one below which was written by Ann. To make it short: did anything happen in the meantime, has there been any telephone conference, is there still any interest out there? I filled out the survey and ask myself wether it makes still sense to submit the form. Regarding the fact I can participate in this year's Galaxy Developers Conference (GCC in Chicago) I would be quite happy if some contacts may arise from this thread or the conference or both in a mutual way (which would be somewhat perfect). The heavily discussed topic regarding time zones should not prevent us from going ahead. Best regards and thanks in advance, Sebastian Schaaf (Munich, Germany) Ann Black-Ziegelbein schrieb: Hello everyone! Here is a link to a brief survey about how you are using, or plan to use Galaxy locally. If you could take a moment to complete the survey, it will help steer the teleconferences as we get going (and also alleviate having to spend time on the call providing the same background info). The results of the survey will be made public off of a new wiki site that Galaxy's Dave Clements is arranging for the group - thanks Dave! Web Survey: https://docs.google.com/spreadsheet/viewform?formkey=dGJZcmxEWDQ3aERPNmlBaDl1eHVsQ3c6MQ Once the teleconference infrastructure details are in place and finalized, I will send out a web poll to see if we can find a time that works for the majority. Thanks, Ann Black-Ziegelbein On 4/27/2012 2:14 PM, Ryan Golhar wrote: This is a great idea. On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein annbl...@eng.uiowa.edu mailto:annbl...@eng.uiowa.edu wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
Thanks Ann for your quick reply, sounds good. I just submitted my info in reply to the online survey. Regarding your issues: don't worry, I think we all suffer from the same things, basically :). No need to apologize. As I stated in the submitted web form we had similar problems with file systems and big data. Maybe a topic for our conversations. Sebastian Ann Black-Ziegelbein schrieb: Hi All - I have dropped the ball on this one. We at Iowa have gotten bogged down in storage issues with galaxy (our existing storage was crashing) and have been spending all my time evaluating different storage solutions under load: zfs, gluster, lustre, nfs for our galaxy and high performance compute cluster. This week our testing and evaluation is almost completed. I have a proposed agenda for our first call I need to circulate as well I have lined up an online web conference solution for us to try which will allow our calls to be recorded and posted for playback. I am actually talking to Dave today and hopefully I will get something out for a call in early to mid July. Sorry folks, I have been busy and it has been hard to get back to this. Ann On 6/28/2012 4:14 AM, Sebastian Schaaf wrote: Also hello to everyone, As I browsed through those tabs which are open for weeks I rediscovered the online survey Interested in Deploying Your Own Local Galaxy? connected to this thread here. The last response I could find in this context was the one below which was written by Ann. To make it short: did anything happen in the meantime, has there been any telephone conference, is there still any interest out there? I filled out the survey and ask myself wether it makes still sense to submit the form. Regarding the fact I can participate in this year's Galaxy Developers Conference (GCC in Chicago) I would be quite happy if some contacts may arise from this thread or the conference or both in a mutual way (which would be somewhat perfect). The heavily discussed topic regarding time zones should not prevent us from going ahead. Best regards and thanks in advance, Sebastian Schaaf (Munich, Germany) Ann Black-Ziegelbein schrieb: Hello everyone! Here is a link to a brief survey about how you are using, or plan to use Galaxy locally. If you could take a moment to complete the survey, it will help steer the teleconferences as we get going (and also alleviate having to spend time on the call providing the same background info). The results of the survey will be made public off of a new wiki site that Galaxy's Dave Clements is arranging for the group - thanks Dave! Web Survey: https://docs.google.com/spreadsheet/viewform?formkey=dGJZcmxEWDQ3aERPNmlBaDl1eHVsQ3c6MQ Once the teleconference infrastructure details are in place and finalized, I will send out a web poll to see if we can find a time that works for the majority. Thanks, Ann Black-Ziegelbein On 4/27/2012 2:14 PM, Ryan Golhar wrote: This is a great idea. On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein annbl...@eng.uiowa.edu mailto:annbl...@eng.uiowa.edu wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Sebastian Schaaf, M.Sc. Bioinformatics Chair of Biometry and Bioinformatics Department of Medical Information Sciences, Biometry and Epidemiology University of Munich Marchioninistr. 15, K U1 (postal) Marchioninistr. 17, U 006 (office) D-81377 Munich (Germany) Tel: +49 89 2180-78229 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
RE: The chat about NZ/AUS communication us here at Otago University (Dunedin, NZ) are very very keen for this. Please email us at edward.hi...@otago.ac.nz if this does decide to take off :) Cheers, Ed ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
Clare, I'm running an AWS Cloudman instance (on US East region) from Sydney for a developing suite of proteomics PTM tools in Perl, for use mainly by http://sydney.edu.au/science/molecular_bioscience/ and http://www.sdu.dk/en/om_sdu/institutter_centre/bmb_biokemi_og_molekylaer_biologi Hard to say if a local group is fully needed yet, but we could try. A multi-site audio or video conference is pretty easy these days. There are always unexpected insights from talking direct to others. I'd be happy to take part. But the main Galaxy dev team in US are so good on the mailing lists, we don't want to impact that. Not a very insightful comment ! I used to be indecisive but now I'm not so sure ... Greg Edwards On Thu, May 10, 2012 at 3:20 PM, Clare Sloggett s...@unimelb.edu.au wrote: Hi all, I'm at one of the places Ross mentions (VLSCI), with Enis - among other things we're deploying Galaxy CloudMan on the new Australian Research Cloud. Just from talking to people I feel that local institutions that have installed their own Galaxy, and are customising it, wrapping tools for the researchers they support etc, do end up struggling with a lot of the same problems. I think though that as Ross is suggesting in a lot of cases these needs could be filled by the existing galaxy-user and galaxy-dev mailing lists (I find sometimes people can be quite hesitant to post a question until they have spent a lot of time on the problem). I do like the idea of a local Australia-New Zealand Galaxy group for developers / techie bioinformaticians, but more for the sake of face-to-face interaction and perhaps local-timezone teleconferences; I don't want to end up just duplicating existing mailing lists. I'm not sure of the best way to make such a group take off or how much interest there would be. If there are other Australian / New Zealand or local timezone groups reading this list and you're interested, let us know! Clare On 30 April 2012 13:35, Ross ross.laza...@gmail.com wrote: To all interested in Dave's suggestion: IMHO, an Australian/New Zealand Galaxy user/deployer/developer group will be worth setting up and will be viable if it solves specific problems that aren't adequately addressed by existing networks and communication channels - otherwise it will be JAFUG (just another fleeting user group) and will likely fizzle due to lack of genuine utility to potential participants. EG: One challenge for us when it comes to (eg) the proposed teleconferences is the tyranny of time zones - being 14 hours ahead of EST eg in Melbourne/Sydney. The other big challenge is that travel to meetings in Europe or the USA is expensive and exhausting, so workshops and hands on training are harder to get to. In general, I think we're probably going to be able to find plenty of problems to do with geographic isolation and maybe even some specific Australian challenges - but let's be clear about exactly what those are before we start building any structures. One problem I keep seeing is that there are many organisations happy to invest in hardware infrastructure, but far less willing to invest in the training and staff development needed for success. Two things I'd like to suggest to help with planning: 1) to get a better idea of scope, it would be very handy to assemble a register of potential organisations and their primary contacts. I already know of some large Australian organisations investing heavily in Galaxy deployment - eg - VLSCI in Melbourne; UQ in Brisbane, CSIRO all over the place, the Victorian DPI, AGRF, and the BakerIDI where I'm based - no doubt there are plenty of others too? 2) to make sure the idea is viable, it would be useful to collect some specific deployment challenges that people are experiencing that some kind of local user's group could help overcome? One focus I have a personal interest in exploring would be in face to face educational activities: eg for local Galaxy instance system administrators? Local tool developers? Local biologist users in specific contexts like short read sequencing? Suggestions welcomed... On Mon, Apr 30, 2012 at 12:37 PM, Dave Clements cleme...@galaxyproject.org wrote: Hi Ryan, Ann, and everyone else I second what Nate says (I always do :-). I too like that it is user driven. And, while I am not a developer, I do plan on being on the call as often as possible. I can also offer my support for logistical and any other support. Ann, please let me know if you want help with getting this going and getting the word out. On a related note, With Matloob's email, we have at least 3 organizations in Australia and New Zealand that are interested. I know that there are many more Galaxy installations in that part of the world (and you have Enis and Ross in Australia now). Would this be a good opportunity to set up the first (to my knowledge)
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
Hi all, I'm at one of the places Ross mentions (VLSCI), with Enis - among other things we're deploying Galaxy CloudMan on the new Australian Research Cloud. Just from talking to people I feel that local institutions that have installed their own Galaxy, and are customising it, wrapping tools for the researchers they support etc, do end up struggling with a lot of the same problems. I think though that as Ross is suggesting in a lot of cases these needs could be filled by the existing galaxy-user and galaxy-dev mailing lists (I find sometimes people can be quite hesitant to post a question until they have spent a lot of time on the problem). I do like the idea of a local Australia-New Zealand Galaxy group for developers / techie bioinformaticians, but more for the sake of face-to-face interaction and perhaps local-timezone teleconferences; I don't want to end up just duplicating existing mailing lists. I'm not sure of the best way to make such a group take off or how much interest there would be. If there are other Australian / New Zealand or local timezone groups reading this list and you're interested, let us know! Clare On 30 April 2012 13:35, Ross ross.laza...@gmail.com wrote: To all interested in Dave's suggestion: IMHO, an Australian/New Zealand Galaxy user/deployer/developer group will be worth setting up and will be viable if it solves specific problems that aren't adequately addressed by existing networks and communication channels - otherwise it will be JAFUG (just another fleeting user group) and will likely fizzle due to lack of genuine utility to potential participants. EG: One challenge for us when it comes to (eg) the proposed teleconferences is the tyranny of time zones - being 14 hours ahead of EST eg in Melbourne/Sydney. The other big challenge is that travel to meetings in Europe or the USA is expensive and exhausting, so workshops and hands on training are harder to get to. In general, I think we're probably going to be able to find plenty of problems to do with geographic isolation and maybe even some specific Australian challenges - but let's be clear about exactly what those are before we start building any structures. One problem I keep seeing is that there are many organisations happy to invest in hardware infrastructure, but far less willing to invest in the training and staff development needed for success. Two things I'd like to suggest to help with planning: 1) to get a better idea of scope, it would be very handy to assemble a register of potential organisations and their primary contacts. I already know of some large Australian organisations investing heavily in Galaxy deployment - eg - VLSCI in Melbourne; UQ in Brisbane, CSIRO all over the place, the Victorian DPI, AGRF, and the BakerIDI where I'm based - no doubt there are plenty of others too? 2) to make sure the idea is viable, it would be useful to collect some specific deployment challenges that people are experiencing that some kind of local user's group could help overcome? One focus I have a personal interest in exploring would be in face to face educational activities: eg for local Galaxy instance system administrators? Local tool developers? Local biologist users in specific contexts like short read sequencing? Suggestions welcomed... On Mon, Apr 30, 2012 at 12:37 PM, Dave Clements cleme...@galaxyproject.org wrote: Hi Ryan, Ann, and everyone else I second what Nate says (I always do :-). I too like that it is user driven. And, while I am not a developer, I do plan on being on the call as often as possible. I can also offer my support for logistical and any other support. Ann, please let me know if you want help with getting this going and getting the word out. On a related note, With Matloob's email, we have at least 3 organizations in Australia and New Zealand that are interested. I know that there are many more Galaxy installations in that part of the world (and you have Enis and Ross in Australia now). Would this be a good opportunity to set up the first (to my knowledge) regional user group? If anyone thinks this is a good idea, please respond (and create a new thread). Finally, Ann, thanks for starting this. Dave C I also that both Ross and Enis are in Australia now On Sun, Apr 29, 2012 at 10:24 AM, Nate Coraor n...@bx.psu.edu wrote: Hi Ryan, I like that it's user-directed, and we could be there to provide input, although if help is needed to organize the call we could probably assist with that. I plan to be on the call as often as my schedule allows, and I believe some of the other developers on the team would also be interested. --nate On Apr 28, 2012, at 8:49 AM, Ryan Golhar wrote: One question - Are the Galaxy developers involved in this or is this for user's only? It may be helpful to have developers on the call to provide information that users do not necessarily have.
Re: [galaxy-dev] Interested in speaking with other, institutions deploying Galaxy locally?
Hello, This is a great idea. I'm interested. Thanks ! Sarah Maman -- Message: 1 Date: Fri, 27 Apr 2012 13:45:16 -0500 From: Ann Black-Ziegelbein annbl...@eng.uiowa.edu To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally? Message-ID: 4f9ae93c.20...@eng.uiowa.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other, institutions deploying Galaxy locally?
We have a small collaboration between institutions in the greater Cape Town region (UCT, UWC, Stellenbosch) on this topic (the so-called Pipelines group). If anyone in South Africa is interested in talking about these topics, please get in touch because we could share expertise. Peter SANBI - UWC On 02/05/2012 09:49, Sarah Maman wrote: Hello, This is a great idea. I'm interested. Thanks ! Sarah Maman -- Message: 1 Date: Fri, 27 Apr 2012 13:45:16 -0500 From: Ann Black-Ziegelbein annbl...@eng.uiowa.edu To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally? Message-ID: 4f9ae93c.20...@eng.uiowa.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
Hello everyone! Here is a link to a brief survey about how you are using, or plan to use Galaxy locally. If you could take a moment to complete the survey, it will help steer the teleconferences as we get going (and also alleviate having to spend time on the call providing the same background info). The results of the survey will be made public off of a new wiki site that Galaxy's Dave Clements is arranging for the group - thanks Dave! Web Survey: https://docs.google.com/spreadsheet/viewform?formkey=dGJZcmxEWDQ3aERPNmlBaDl1eHVsQ3c6MQ Once the teleconference infrastructure details are in place and finalized, I will send out a web poll to see if we can find a time that works for the majority. Thanks, Ann Black-Ziegelbein On 4/27/2012 2:14 PM, Ryan Golhar wrote: This is a great idea. On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein annbl...@eng.uiowa.edu mailto:annbl...@eng.uiowa.edu wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
Ann, I'm interested. I'm running a Galaxy instance on AWS Cloud, using the standard Galaxy Cloudman. Based in Sydney, Aus and also users at SDU, Odense, Denmark. My timezone for a conf call would be UTC +10 as for some others here. Greg Edwards On Sat, Apr 28, 2012 at 4:45 AM, Ann Black-Ziegelbein annbl...@eng.uiowa.edu wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein __**_ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Greg Edwards, Port Jackson Bioinformatics gedwar...@gmail.com ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
On 04/27/2012 08:45 PM, Ann Black-Ziegelbein wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. I'm interested. We have different local Galaxy running and we are on the way to connect them to our sequencing and genotyping platform. Glad to partecipate, Mauro -- Gianmauro Cuccuru CRS4 Bioinformatica POLARIS Edificio 3, Loc. Piscina Manna 09010 Pula (CA), Italy http://www.bioinformatica.crs4.it phone: +390709250428 email: gma...@crs4.it Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
Hi Ann I am definitively interested in any form of collaboration - thank you very much for bringing up this idea! However, I also share some of the concerns which have been raised by others. Even in Europe, we sometimes struggle to coordinate a conference call with the Americas and very often the quality is so bad it is impossible to have a discussion. Also, looking at the success of your original e-mail, now imagine a conference call with more than 20 participants... You can call me 'old fashion' but I prefer face-to-face meetings. So I am looking very much forward to Chicago this summer. I am aware, due to costs and other reasons not everybody will be able to attend GCC. Having regional Galaxy meetings is one solution. Together with the Galaxy developers, I intended to organize an European Galaxy workshop as part of ECCB2012 in Basel in September. Unfortunately, the ECCB organizers did approve our proposal. I will now organize a smaller (Swiss) workshop in fall which will be open to everybody. I'll keep the list posted as soon as it has been finalized. Nevertheless, I hope we can create an even better community and I will make any effort to take part in any upcoming Galaxy conference calls. Regards, Hans On 04/27/2012 08:45 PM, Ann Black-Ziegelbein wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
Hi, We have two galaxy instances installed within our institute, and I am very interested in communicating with other galaxy users. Please count me in. Zhibin Lu Bioinformatics Support: Databases Applications Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 Tel: 647-260-7944 Toll-free: 1-866-678-6427 www.oicr.on.ca Date: Fri, 27 Apr 2012 13:45:16 -0500 From: annbl...@eng.uiowa.edu To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally? Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
Agreed. User driven is good. Having developer(s) available to answer questions would be helpful...that's what I was alluding to... On Sun, Apr 29, 2012 at 10:37 PM, Dave Clements cleme...@galaxyproject.orgwrote: Hi Ryan, Ann, and everyone else I second what Nate says (I always do :-). I too like that it is user driven. And, while I am not a developer, I do plan on being on the call as often as possible. I can also offer my support for logistical and any other support. Ann, please let me know if you want help with getting this going and getting the word out. On a related note, With Matloob's email, we have at least 3 organizations in Australia and New Zealand that are interested. I know that there are many more Galaxy installations in that part of the world (and you have Enis and Ross in Australia now). Would this be a good opportunity to set up the first (to my knowledge) regional user group? If anyone thinks this is a good idea, please respond (and create a new thread). Finally, Ann, thanks for starting this. Dave C I also that both Ross and Enis are in Australia now On Sun, Apr 29, 2012 at 10:24 AM, Nate Coraor n...@bx.psu.edu wrote: Hi Ryan, I like that it's user-directed, and we could be there to provide input, although if help is needed to organize the call we could probably assist with that. I plan to be on the call as often as my schedule allows, and I believe some of the other developers on the team would also be interested. --nate On Apr 28, 2012, at 8:49 AM, Ryan Golhar wrote: One question - Are the Galaxy developers involved in this or is this for user's only? It may be helpful to have developers on the call to provide information that users do not necessarily have. -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
I would like to thank everyone for their responses! I am working on a few things to hopefully get us going in the right direction: 1) a brief online web survey for everyone to fill out that will help us gauge the background of those interested in participation and help steer content for the first call. For example, what stage your local Galaxy deployment is in ( running for several years with 20+ users, no running local Galaxy but interested in hosting one, currently installing and configuring, etc). How many people are you targeting using Galaxy? What problem areas have you hit? What customizations have you done? What areas are you interested in learning more about in these calls? etc.) The results of the survey will be published out to the group. 2) I am working on getting a teleconference with international numbers arranged. I like the idea of having regional groups and maybe summaries/any presentation slides can be posted to do cross regional sharing. At the same time - anyone interested (from any geographic region) is welcome to join - time zones may not be convenient, however, but we will do our best. 3) I will send out a poll to see if we can find the *best* time for our first call. Yes, this will be difficult - but we will pick a time that works for the majority. Stay tuned and looking forward to our first call. Dave, as always, thanks for your help - I will be contacting you shortly. Ann On 4/30/2012 9:39 AM, Ryan Golhar wrote: Agreed. User driven is good. Having developer(s) available to answer questions would be helpful...that's what I was alluding to... On Sun, Apr 29, 2012 at 10:37 PM, Dave Clements cleme...@galaxyproject.org mailto:cleme...@galaxyproject.org wrote: Hi Ryan, Ann, and everyone else I second what Nate says (I always do :-). I too like that it is user driven. And, while I am not a developer, I do plan on being on the call as often as possible. I can also offer my support for logistical and any other support. Ann, please let me know if you want help with getting this going and getting the word out. On a related note, With Matloob's email, we have at least 3 organizations in Australia and New Zealand that are interested. I know that there are many more Galaxy installations in that part of the world (and you have Enis and Ross in Australia now). Would this be a good opportunity to set up the first (to my knowledge) regional user group? If anyone thinks this is a good idea, please respond (and create a new thread). Finally, Ann, thanks for starting this. Dave C I also that both Ross and Enis are in Australia now On Sun, Apr 29, 2012 at 10:24 AM, Nate Coraor n...@bx.psu.edu mailto:n...@bx.psu.edu wrote: Hi Ryan, I like that it's user-directed, and we could be there to provide input, although if help is needed to organize the call we could probably assist with that. I plan to be on the call as often as my schedule allows, and I believe some of the other developers on the team would also be interested. --nate On Apr 28, 2012, at 8:49 AM, Ryan Golhar wrote: One question - Are the Galaxy developers involved in this or is this for user's only? It may be helpful to have developers on the call to provide information that users do not necessarily have. -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
Hi, all, We are in the process of setting up Galaxy as a big university framework for the entire university and world-wide free academic access. We currently have a portal (www.bioportal.uio.no) which is bioinformatics oriented. The Galaxy we are setting up will give access to more than 100 applications and will include the following features: - Apache proxy enabled - implemented - PostgreSQL located in another host - - implemented - sending jobs to a cluster (using SLURM, drmaa) - implemented - identification via SAML2 - (not OpenID) - implementaiton phase now, problems with reading the response from IdP If any of you has experience in pysaml2 + WSGI, please let me know. In turn, I am willing to share our experience so far with the issues above. Best regards Nikolay On Sun, 29 Apr 2012 17:11:05 +1200, Edward Hills ehills...@gmail.com wrote: Hi Ann, We are in the process of doing the same thing here at the University of Otago (New Zealand). If we are able to sort something via the timezone difference (we are GMT+12, first to see the sun!) we would very much be interested. Cheers, Ed Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Nikolay Vazov, PhD Research Computing Centre - http://hpc.uio.no USIT, University of Oslo ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
Hi Ryan, I like that it's user-directed, and we could be there to provide input, although if help is needed to organize the call we could probably assist with that. I plan to be on the call as often as my schedule allows, and I believe some of the other developers on the team would also be interested. --nate On Apr 28, 2012, at 8:49 AM, Ryan Golhar wrote: One question - Are the Galaxy developers involved in this or is this for user's only? It may be helpful to have developers on the call to provide information that users do not necessarily have. On Fri, Apr 27, 2012 at 8:21 PM, steve.mcma...@csiro.au wrote: Sounds like a good idea to me. I'm sure the time will be awkward due to the time zone difference. I'm at UTC+10. Regards. Steve McMahon Solutions architect senior systems administrator ASC Cluster Services Information Management Technology (IMT) CSIRO Phone: +61-2-62142968 | Mobile: +61-4-00779318 steve.mcma...@csiro.au | www.csiro.au PO Box 225, DICKSON ACT 2602 1 Wilf Crane Crescent, Yarralumla ACT 2600 -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Ann Black-Ziegelbein Sent: Saturday, 28 April 2012 4:45 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally? Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
We've also started a local deployment for University of Illinois Urbana-Champaign. So I would be interested in participating. Chris On Apr 27, 2012, at 2:32 PM, David Hoover hoove...@helix.nih.gov wrote: Not a bad idea. Most of the conversations on this list are very limited and detailed in scope, dealing with the minutia of tools and variables. There isn't much on the bird's eye view. I'm in. On Apr 27, 2012, at 2:45 PM, Ann Black-Ziegelbein wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
Hi Ryan, Ann, and everyone else I second what Nate says (I always do :-). I too like that it is user driven. And, while I am not a developer, I do plan on being on the call as often as possible. I can also offer my support for logistical and any other support. Ann, please let me know if you want help with getting this going and getting the word out. On a related note, With Matloob's email, we have at least 3 organizations in Australia and New Zealand that are interested. I know that there are many more Galaxy installations in that part of the world (and you have Enis and Ross in Australia now). Would this be a good opportunity to set up the first (to my knowledge) regional user group? If anyone thinks this is a good idea, please respond (and create a new thread). Finally, Ann, thanks for starting this. Dave C I also that both Ross and Enis are in Australia now On Sun, Apr 29, 2012 at 10:24 AM, Nate Coraor n...@bx.psu.edu wrote: Hi Ryan, I like that it's user-directed, and we could be there to provide input, although if help is needed to organize the call we could probably assist with that. I plan to be on the call as often as my schedule allows, and I believe some of the other developers on the team would also be interested. --nate On Apr 28, 2012, at 8:49 AM, Ryan Golhar wrote: One question - Are the Galaxy developers involved in this or is this for user's only? It may be helpful to have developers on the call to provide information that users do not necessarily have. -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
To all interested in Dave's suggestion: IMHO, an Australian/New Zealand Galaxy user/deployer/developer group will be worth setting up and will be viable if it solves specific problems that aren't adequately addressed by existing networks and communication channels - otherwise it will be JAFUG (just another fleeting user group) and will likely fizzle due to lack of genuine utility to potential participants. EG: One challenge for us when it comes to (eg) the proposed teleconferences is the tyranny of time zones - being 14 hours ahead of EST eg in Melbourne/Sydney. The other big challenge is that travel to meetings in Europe or the USA is expensive and exhausting, so workshops and hands on training are harder to get to. In general, I think we're probably going to be able to find plenty of problems to do with geographic isolation and maybe even some specific Australian challenges - but let's be clear about exactly what those are before we start building any structures. One problem I keep seeing is that there are many organisations happy to invest in hardware infrastructure, but far less willing to invest in the training and staff development needed for success. Two things I'd like to suggest to help with planning: 1) to get a better idea of scope, it would be very handy to assemble a register of potential organisations and their primary contacts. I already know of some large Australian organisations investing heavily in Galaxy deployment - eg - VLSCI in Melbourne; UQ in Brisbane, CSIRO all over the place, the Victorian DPI, AGRF, and the BakerIDI where I'm based - no doubt there are plenty of others too? 2) to make sure the idea is viable, it would be useful to collect some specific deployment challenges that people are experiencing that some kind of local user's group could help overcome? One focus I have a personal interest in exploring would be in face to face educational activities: eg for local Galaxy instance system administrators? Local tool developers? Local biologist users in specific contexts like short read sequencing? Suggestions welcomed... On Mon, Apr 30, 2012 at 12:37 PM, Dave Clements cleme...@galaxyproject.org wrote: Hi Ryan, Ann, and everyone else I second what Nate says (I always do :-). I too like that it is user driven. And, while I am not a developer, I do plan on being on the call as often as possible. I can also offer my support for logistical and any other support. Ann, please let me know if you want help with getting this going and getting the word out. On a related note, With Matloob's email, we have at least 3 organizations in Australia and New Zealand that are interested. I know that there are many more Galaxy installations in that part of the world (and you have Enis and Ross in Australia now). Would this be a good opportunity to set up the first (to my knowledge) regional user group? If anyone thinks this is a good idea, please respond (and create a new thread). Finally, Ann, thanks for starting this. Dave C I also that both Ross and Enis are in Australia now On Sun, Apr 29, 2012 at 10:24 AM, Nate Coraor n...@bx.psu.edu wrote: Hi Ryan, I like that it's user-directed, and we could be there to provide input, although if help is needed to organize the call we could probably assist with that. I plan to be on the call as often as my schedule allows, and I believe some of the other developers on the team would also be interested. --nate On Apr 28, 2012, at 8:49 AM, Ryan Golhar wrote: One question - Are the Galaxy developers involved in this or is this for user's only? It may be helpful to have developers on the call to provide information that users do not necessarily have. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
One question - Are the Galaxy developers involved in this or is this for user's only? It may be helpful to have developers on the call to provide information that users do not necessarily have. On Fri, Apr 27, 2012 at 8:21 PM, steve.mcma...@csiro.au wrote: Sounds like a good idea to me. I'm sure the time will be awkward due to the time zone difference. I'm at UTC+10. Regards. Steve McMahon Solutions architect senior systems administrator ASC Cluster Services Information Management Technology (IMT) CSIRO Phone: +61-2-62142968 | Mobile: +61-4-00779318 steve.mcma...@csiro.au | www.csiro.au PO Box 225, DICKSON ACT 2602 1 Wilf Crane Crescent, Yarralumla ACT 2600 -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto: galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Ann Black-Ziegelbein Sent: Saturday, 28 April 2012 4:45 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally? Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
Hi Ann, We are in the process of doing the same thing here at the University of Otago (New Zealand). If we are able to sort something via the timezone difference (we are GMT+12, first to see the sun!) we would very much be interested. Cheers, Ed Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
This is a great idea. On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein annbl...@eng.uiowa.edu wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein __**_ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
I'm interested On Apr 27, 2012, at 3:14 PM, Ryan Golhar wrote: This is a great idea. On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein annbl...@eng.uiowa.edumailto:annbl...@eng.uiowa.edu wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Brad Langhorst langho...@neb.commailto:langho...@neb.com 978-380-7564 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
Cool idea. I am very interested in it. One question: how could we attend the conference since we all at different place? Cheers, Tyler On Fri, Apr 27, 2012 at 12:33 PM, Mohammad Heydarian mheyd...@jhmi.eduwrote: Great idea. In! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 414 Hunterian Baltimore, MD 21205 On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein annbl...@eng.uiowa.edu wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein __**_ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
Thanks everyone! Glad to find some common interest. I will see if I can arrange an initial call. Hi Tyler - I was hoping we could just do a voice conference call. It would be great to meet those face to face at the Galaxy Conference in Chicago if some are attending. Thanks! Ann On 4/27/2012 3:07 PM, JIE CHEN wrote: Cool idea. I am very interested in it. One question: how could we attend the conference since we all at different place? Cheers, Tyler On Fri, Apr 27, 2012 at 12:33 PM, Mohammad Heydarian mheyd...@jhmi.edu mailto:mheyd...@jhmi.edu wrote: Great idea. In! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 414 Hunterian Baltimore, MD 21205 On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein annbl...@eng.uiowa.edu mailto:annbl...@eng.uiowa.edu wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
I'm interested too. On 27 Apr 2012, at 21:13, Ann Black-Ziegelbein wrote: Thanks everyone! Glad to find some common interest. I will see if I can arrange an initial call. Hi Tyler - I was hoping we could just do a voice conference call. It would be great to meet those face to face at the Galaxy Conference in Chicago if some are attending. Thanks! Ann On 4/27/2012 3:07 PM, JIE CHEN wrote: Cool idea. I am very interested in it. One question: how could we attend the conference since we all at different place? Cheers, Tyler On Fri, Apr 27, 2012 at 12:33 PM, Mohammad Heydarian mheyd...@jhmi.edu wrote: Great idea. In! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 414 Hunterian Baltimore, MD 21205 On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein annbl...@eng.uiowa.edu wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Anne Pajon, Ph.D. Cancer Research UK - Cambridge Research Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pa...@cancer.org.uk | +44 (0)7958 511 353 NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered in England and Wales Company Registered Number: 4325234. Registered Charity Number: 1089464 and Scotland SC041666 Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
Here's another interested! On Apr 27, 2012, at 8:45 PM, Ann Black-Ziegelbein wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ /* Davide Cittaro, PhD Head of Bioinformatics Core Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute Via Olgettina 58 20132 Milano Italy Office: +39 02 26439140 Mail: cittaro.dav...@hsr.itmailto:cittaro.dav...@hsr.it Skype: daweonline */ http://www.5xmille.org/[cid:firma3e79.jpg]http://www.sanraffaele.org Disclaimer added by CodeTwo Exchange Rules 2007 www.codetwo.comhttp://www.codetwo.com inline: firma3e79.jpg___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
We are interested too. Thanks Ann for taking the initiative. -- Shantanu On Apr 27, 2012, at 3:38 PM, Anne Pajon wrote: I'm interested too. On 27 Apr 2012, at 21:13, Ann Black-Ziegelbein wrote: Thanks everyone! Glad to find some common interest. I will see if I can arrange an initial call. Hi Tyler - I was hoping we could just do a voice conference call. It would be great to meet those face to face at the Galaxy Conference in Chicago if some are attending. Thanks! Ann On 4/27/2012 3:07 PM, JIE CHEN wrote: Cool idea. I am very interested in it. One question: how could we attend the conference since we all at different place? Cheers, Tyler On Fri, Apr 27, 2012 at 12:33 PM, Mohammad Heydarian mheyd...@jhmi.edu wrote: Great idea. In! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 414 Hunterian Baltimore, MD 21205 On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein annbl...@eng.uiowa.edu wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Anne Pajon, Ph.D. Cancer Research UK - Cambridge Research Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pa...@cancer.org.uk | +44 (0)7958 511 353 NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered in England and Wales Company Registered Number: 4325234. Registered Charity Number: 1089464 and Scotland SC041666 Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
