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From: Victor U. <ll...@gm...> - 2017-04-03 23:33:15
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Dear Tripal Developers and Users, I hope everyone is doing great. We will have our monthly Tripal Developer and User meeting this Friday, April 7th. The meeting is open for everyone. If you have not previously attended, please consider attending especially if you are considering development of custom extensions. The goal of the meeting is to share news about Tripal, provide an opportunity to share ideas, ask questions, provide training, and to advertise what you are doing. The meeting start time and connection details follow below. The meeting will take approximately one hour. Below is the link to the agenda for the upcoming meeting. If you have something you'd like to discuss please add it (and include your name): Tripal User's Meeting April/07/2017: https://docs.google.com/document/d/1WMuzjrAOCOJfOEg9ZW8ywEr3B7vofCoHvOI0vDxn5D8/edit?usp=sharing <https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1WMuzjrAOCOJfOEg9ZW8ywEr3B7vofCoHvOI0vDxn5D8_edit-3Fusp-3Dsharing&d=DwMFAg&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=IgTeSNohJJLqxRy-1sJO1A&m=ZlrD2DxvoSM_0BBHOqAdsf60yhblUpOPVOFUDz72WSo&s=wisRHQR4bq-yFbtdbZAj3XHkUXkWFRUH4g4x82gp04o&e=> If you want to check our last meeting notes for the Tripal User's Meeting, please visit this link: http://tripal.info/meetings/users/summary <https://urldefense.proofpoint.com/v2/url?u=http-3A__tripal.info_meetings_users_summary&d=DwMFAg&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=IgTeSNohJJLqxRy-1sJO1A&m=ZlrD2DxvoSM_0BBHOqAdsf60yhblUpOPVOFUDz72WSo&s=71y0oEYATfrqAW3IwuTAgUiuSBLXW0soxvJGIpxv-uk&e=> Victor Unda-- ---- Pacific Time, PT PST (UTC -7) Fri, April 7, 2017 8:00 am Central European Time, CET CET (UTC +1) Fri, April 7, 2017 4:00 pm Eastern Time, ET EST (UTC -4) Fri, April 7, 2017 11:00 am Central Time, CT CST (UTC -5) Fri, April 7, 2017 10:00 am Regina, Canada CST (UTC -6) Fri, April 7, 2017 9:00 am Pacific Standard Time, PST PST (UTC -8) Fri, April 7, 2017 7:00 am China Standard Time, CST CST (UTC +8) Sat, April 7, 2017 11:00 midn Connection Details: Please join my meeting from your computer, tablet or smartphone. https://global.gotomeeting.com/join/762905221 <https://urldefense.proofpoint.com/v2/url?u=https-3A__global.gotomeeting.com_join_762905221&d=DwMFAg&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=IgTeSNohJJLqxRy-1sJO1A&m=ZlrD2DxvoSM_0BBHOqAdsf60yhblUpOPVOFUDz72WSo&s=xjNOoXgr7WR4CbhQZ_pLCYgKcZ7owchzFgXI8LibFn0&e=> You can also dial in using your phone. United States: +1 (312) 757-3121 Access Code: 762-905-221 |
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From: Stephen F. <spf...@gm...> - 2017-04-01 21:33:51
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Dear Tripal Community,
Tripal v2.1 is now available! This release provides major bug fixes as
well as support for Chado v1.3. Here are links to upgrade instructions:
* Upgrade from Tripal v2.0 to v2.1:
http://tripal.info/tutorials/v2.x/upgrade_2.0_to_2.1
* Upgrade from Tripal v1.1 to v2.1:
http://tripal.info/tutorials/v2.x/upgrade_6.11_to_2.1
Please remember to back up your sites before upgrading and it's always
best to try your upgrade on a developmental copy first.
Additionally, we have made new releases of the Tripal Analysis Blast,
GO, InterPro and KEGG modules. Please consider upgrading those as well
if you use them. Instructions for updating those are also provided in
the links above. Some new visualizations have been provided for some
of these modules thanks to contributions by some of you!
The Drupal issue queue will no longer be used to track bugs or feature
requests. If you notice any problems with this release please help us
by reporting them to our GitHub issue queue:
https://github.com/tripal/tripal/issues
We have added a new 'Powered by Tripal' block in this new version.
Please consider adding this block to the footer section of your site.
If you prefer to use something other than the block I've attached
several images to this email for your to consider placing on your sites.
Thank you to those who provided bug fixes and pull requests!
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From: Stephen F. <spf...@gm...> - 2017-03-27 15:40:52
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Hi All, Will anyone be attending the Plant Biology meeting in Hawaii this summer (http://plantbiology.aspb.org/)? If we have enough interest I'd like to put together a hackathon or training meeting. Please let me know if you would be interested and could attend. Thanks, Stephen |
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From: Stephen F. <spf...@gm...> - 2017-03-24 15:43:42
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Hi All, I was hoping to arrange a training meeting this month for our Tripal community but it was not possible. So, I'd like to organize one for Friday the 14th of April. Some topics include * How to use of the bulk loader to load tab delimited files. * How to develop your own extensions for Tripal v3. If you have any other topic suggestions or prefer one of these over the other please let me know. I'm suggesting we hold the training meeting a week after our normal Tripal User's meeting (will be on 4/7) but at the same time at 8am PDT (or click this link to see the time of the meeting in your time zone: https://www.timeanddate.com/worldclock/fixedtime.html?msg=Tripal+Training+Meeting&iso=20170414T08&p1=234&ah=2) Also, if this time is not conducive we can be flexible based on responses received. Thanks, Stephen |
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From: Stephen F. <spf...@gm...> - 2017-03-04 17:39:44
|
Hi Michael, We'll add it to our issue queue. If you would like to submit your fix as a pull request on Tripal's github project page then we can review your fix and merge it in if it looks like there are no other side effects: https://github.com/tripal/tripal Stephen On 3/3/2017 4:53 AM, Michael Dondrup wrote: > Hi Stephen, > > I have checked with 7.x-2.x and updated the issue, unfortunately the update didn’t have an effect. > I also added a quick work around, but I am not sure if that breaks other stuff. > > Cheers > Michael > > >> On Mar 2, 2017, at 6:53 PM, Stephen Ficklin <spf...@gm...> wrote: >> >> Hi Michael, >> >> I've commented on the Issue item, which I believe is the same one? >> https://www.drupal.org/node/2856973 >> >> In brief. We have notice this problem in the past and I thought we fixed it on the development branch. Are you using the development branch or version 2.0? If you are using the development branch and this is happening then we need to fix it. >> Stephen >> >> On 3/1/2017 5:33 AM, Michael Dondrup wrote: >>> Hi, >>> Unfortunately I have discovered another problem. Editing a feature, >>> and then saving it apparently removes all the features relationships, >>> without the ability to restore them manually. >>> Has this been reported? >>> >>> Michael >>> >>> >>> >>> Michael Dondrup >>> Researcher >>> Sea Lice Research Centre >>> Department of Informatics >>> University of Bergen >>> Thormøhlensgate 55, N-5008 Bergen, >>> Norway >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, SlashDot.org! >>> http://sdm.link/slashdot >>> >>> >>> _______________________________________________ >>> Gmod-tripal-devel mailing list >>> >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, SlashDot.org! http://sdm.link/slashdot_______________________________________________ >> Gmod-tripal-devel mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel |
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From: Michael D. <mic...@ii...> - 2017-03-03 13:09:14
|
Hi Stephen, I have checked with 7.x-2.x and updated the issue, unfortunately the update didn’t have an effect. I also added a quick work around, but I am not sure if that breaks other stuff. Cheers Michael > On Mar 2, 2017, at 6:53 PM, Stephen Ficklin <spf...@gm...> wrote: > > Hi Michael, > > I've commented on the Issue item, which I believe is the same one? > https://www.drupal.org/node/2856973 > > In brief. We have notice this problem in the past and I thought we fixed it on the development branch. Are you using the development branch or version 2.0? If you are using the development branch and this is happening then we need to fix it. > Stephen > > On 3/1/2017 5:33 AM, Michael Dondrup wrote: >> Hi, >> Unfortunately I have discovered another problem. Editing a feature, >> and then saving it apparently removes all the features relationships, >> without the ability to restore them manually. >> Has this been reported? >> >> Michael >> >> >> >> Michael Dondrup >> Researcher >> Sea Lice Research Centre >> Department of Informatics >> University of Bergen >> Thormøhlensgate 55, N-5008 Bergen, >> Norway >> >> >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, SlashDot.org! >> http://sdm.link/slashdot >> >> >> _______________________________________________ >> Gmod-tripal-devel mailing list >> >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot_______________________________________________ > Gmod-tripal-devel mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel |
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From: Stephen F. <spf...@gm...> - 2017-03-02 17:53:05
|
Hi Michael, I've commented on the Issue item, which I believe is the same one? https://www.drupal.org/node/2856973 In brief. We have notice this problem in the past and I thought we fixed it on the development branch. Are you using the development branch or version 2.0? If you are using the development branch and this is happening then we need to fix it. Stephen On 3/1/2017 5:33 AM, Michael Dondrup wrote: > Hi, > Unfortunately I have discovered another problem. Editing a feature, > and then saving it apparently removes all the features relationships, > without the ability to restore them manually. > Has this been reported? > > Michael > > > > Michael Dondrup > Researcher > Sea Lice Research Centre > Department of Informatics > University of Bergen > Thormøhlensgate 55, N-5008 Bergen, > Norway > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > > > _______________________________________________ > Gmod-tripal-devel mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel |
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From: Michael D. <mic...@ii...> - 2017-03-01 13:33:59
|
Hi, Unfortunately I have discovered another problem. Editing a feature, and then saving it apparently removes all the features relationships, without the ability to restore them manually. Has this been reported? Michael Michael Dondrup Researcher Sea Lice Research Centre Department of Informatics University of Bergen Thormøhlensgate 55, N-5008 Bergen, Norway |
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From: Victor U. <ll...@gm...> - 2017-02-28 22:36:37
|
Dear Tripal Developers and Users, I hope everyone is doing great. We will have our monthly Tripal Developer and User meeting this Friday, March 3rd. The meeting is open for everyone. If you have not previously attended, please consider attending especially if you are considering development of custom extensions. The goal of the meeting is to share news about Tripal, provide an opportunity to share ideas, ask questions, provide training, and to advertise what you are doing. The meeting start time and connection details follow below. The meeting will take approximately one hour. Below is the link to the agenda. https://docs.google.com/document/d/1TzKXs11S10TXXqfxK3GKP1Bkm5VZ2Gui5exRlrvw-3k/edit?usp=sharing If you have something you'd like to discuss please add it (and include your name): Best, Victor Unda Pacific Time, PT PST (UTC -8) Fri, Feb 3, 2017 8:00 am Central European Time, CET CET (UTC +1) Fri, Feb 3, 2017 5:00 pm Eastern Time, ET EST (UTC -5) Fri, Feb 3, 2017 11:00 am Central Time, CT CST (UTC -6) Fri, Feb 3, 2017 10:00 am Regina, Canada CST (UTC -6) Fri, Feb 3, 2017 10:00 am Pacific Standard Time, PST PST (UTC -8) Fri, Feb 3, 2017 8:00 am China Standard Time, CST CST (UTC +8) Sat, Feb 4, 2017 12:00 midn Connection Details: Please join my meeting from your computer, tablet or smartphone. https://global.gotomeeting.com/join/762905221 <https://urldefense.proofpoint.com/v2/url?u=https-3A__global.gotomeeting.com_join_762905221&d=DwMD-g&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=IgTeSNohJJLqxRy-1sJO1A&m=BHeUEzvLJuOHeCA8im7i9il1lXBhXPQgpRunCyiQV2I&s=NzNF7FDKCsrkV8jy9UaDh321nwtfsEm_n9To3Mcor6Q&e=> You can also dial in using your phone. United States: +1 (312) 757-3121 Access Code: 762-905-221 |
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From: Sudhansu D. <sd...@nc...> - 2017-02-16 22:26:41
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Hello, In our gene feature page I have a panel called 'Expression' coming from the tripal_analysis_expression module. This comes from the '#tripal_toc_title' => 'Expression' defined in $node->contents array in the hook_node_view. The effect of this is that it appears as the panel label _as well as_ the page title. I want to have the page title for this panel modified to 'Expression ($feature->name)' while keeping the panel label unaltered. How do I accomplish that? Is there another markup element like '#tripal_toc_title' that specifies the page title that I can define here? Even suppressing the page title while not affecting the panel label would serve my purpose. (I have already tried putting '($feature->name)' below the page title: It works but not what I ideally want to do.) Thanks. Sudhansu Dash |
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From: Stephen F. <spf...@gm...> - 2017-02-11 07:17:02
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Dear Tripal Community, We are happy to announce the release of Tripal v3.0-beta1! Here are some quick links: Tripal v3.x User's Guide: http://tripal.info/tutorials/v3.x Tripal v3.x Download Page at Drupal.org: https://www.drupal.org/project/tripal/releases/7.x-3.0-beta1 The Tripal Issue Queue: https://www.drupal.org/project/issues/tripal This release represents a major improvement over the 7.x-3.0-alpha1 release. This represents a stable design for Tripal v3, although perhaps a still buggy implementation. We expect future v3 beta releases to be primarily bug fixes and addition of some outstanding features that need completion. _Remember, this is a beta release version!_ We expect you will find bugs. We recommend testing Tripal v3.0-beta1 on a development server. Future updates to the beta version will provide Drupal based updates. These will ensure that periodic updates can easily transition your Tripal v3.0-beta site to a full stable Tripal v3.0 site once the stable version is finally released (expected in May 2017). Please help us speed our stable release by reporting any bugs you may find with instructions for how to reproduce them to our issue Queue above or ask questions on our mailing lists. This release provides the following: 1. All Tripal content types are now implemented using Entities rather than Nodes. 2. Tripal content types no longer follow the Chado schema structure. Content types are now more intuitive and based on controlled vocabulary terms. For example, previously feature pages would provide content for genes, SNPs, mRNA, genetic markers, etc. Now each of those types can be their own Tripal Content Typel 3. Site admins can create as many content types as they have data in their site. There is no limit to the type and number of content types. 4. A new Storage API layer has been added to separate Tripal from Chado. Chado still serves as the primary storage location for data, but the new layer will allow for integration of data from other data sources. This beta version does not yet support any other data storage other than Chado. The full stable v3.0 release will. 5. Ancillary data about Tripal Content Types are now "attached" as fields to Entities. This allows the site admin to full customize the layout of the site without writing PHP templates. Templates can still be used if desired, but now it's possible to create a much more custom layout than previously. 6. This version now provides the first introduction of RESTful web services to Tripal. Remote programmers can now access data from a Tripal site using any scripting language they desire to retrieve data formatted in JSON-LD using the W3C Hydra vocabulary. Web services still require implementation of access controls, and a much richer querying structure. The full stable v3.0 release will have a mature RESTFul web services. 7. To assist with layout of new content types with lots of attached fields a new tripal_ds module is provided that automatically creates new layouts for each content type using Display Suites. The layout is designed to resemble the Tripal v2 template based layout for consistency. But site admins are free to change these layouts using the Tripal Content Type graphical interface. 8. Tripal v3 provides a migration tool to help ease the burden of converting your Tripal v2 nodes over to Tripal v3. It especially allows for use of your custom Tripal v2 templates even with Tripal v3 Entities. This will allow for faster upgrade to v3 while still affording a gradual transition from v2 templates to v3 layouts. Some current limitations: 1. The User's Guide is still not complete, although it will walk you through installation and setup of a very simple example genomics website. 2. The Developer's Handbook and API documentation are not yet available. 3. The RESTful web services currently lack access controls and a more complicated query interface is needed. These updates will be made in a later beta release and the stable version. 4. Integration of non Chado data stores is not yet ready. This should be ready in a future beta release and in the final stable version. 5. Bugs! Please let us know what you find. |
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From: Victor U. <ll...@gm...> - 2017-02-01 06:00:56
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Dear Tripal Developers and Users, We will have our monthly Tripal Developer and User meeting this Friday, Feb 3rd. The meeting is open for everyone. If you have not previously attended, please consider attending especially if you are considering development of custom extensions. The goal of the meeting is to share news about Tripal, provide an opportunity to share ideas, ask questions, provide training, and to advertise what you are doing. The meeting start time and connection details follow below. The meeting will take approximately one hour. The agenda is currently blank but we will add to it before the meeting on Friday. If you have something you'd like to discuss please add it (and include your name): https://docs.google.com/document/d/12TB8bWPwHyufPN3lDKfZGTJx0OOrP 6rjORqKetb1kY8/edit?usp=sharing For those who couldn’t attend last month's meeting and Hackathon at the Plant and Animal Genome Conference in San Diego you can read those meeting notes by visiting this link: http://tripal.info/meetings/users/summary Best, Victor Unda Pacific Time, PT PST (UTC -8) Fri, Feb 3, 2017 8:00 am Central European Time, CET CET (UTC +1) Fri, Feb 3, 2017 5:00 pm Eastern Time, ET EST (UTC -5) Fri, Feb 3, 2017 11:00 am Central Time, CT CST (UTC -6) Fri, Feb 3, 2017 10:00 am Regina, Canada CST (UTC -6) Fri, Feb 3, 2017 10:00 am Pacific Standard Time, PST PST (UTC -8) Fri, Feb 3, 2017 8:00 am China Standard Time, CST CST (UTC +8) Sat, Feb 4, 2017 12:00 midn Connection Details: Please join my meeting from your computer, tablet or smartphone. https://global.gotomeeting.com/join/762905221 You can also dial in using your phone. United States: +1 (312) 757-3121 Access Code: 762-905-221 |
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From: Stephen F. <spf...@gm...> - 2017-02-01 05:25:55
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Hi All, For those of you anticipating a Tripal v3.0-beta release today I wanted to let you know that it is very close but not quite ready. We are actively working to get this release out as soon as possible so that you can begin testing fresh installs or migrations. We have pushed our expected release date to February 10th. I will keep you informed of our progress. Thanks for your patience, Stephen |
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From: Kucheran, L. S. <la...@ma...> - 2016-12-05 23:04:55
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Hi Everyone, We have been assigned Royal Palm Salon 4 at the Town & Country for both Thursday, January 12 (Hackathon) and Friday, January 13 (Meeting). Here is the Tentative Agenda: https://docs.google.com/document/d/1e8g0NfihOzBDO0kp0OTrao1vgn1ODkrm394b5mTwk8w/edit?usp=sharing Please add your name to the attending list if your planning on attending. Also, I would love any suggestions people have for Hackathon or Discussion topics (2nd page)! Hope to see you there! ~Lacey ------------------------------------------------------ Lacey-Anne Sanderson Bioinformaticist Pulse Crop Breeding and Genetics Phone: (306) 966-3208<tel://966-3208> Email: lac...@sh...<mailto:lac...@sh...> Room 2C33 Agriculture Department of Plant Sciences University of Saskatchewan On October 25, 2016 at 11:43:25 AM, Kucheran, Lacey Sanderson (la...@ma...<mailto:la...@ma...>) wrote: Hi Everyone, I’m excited to say there is enough interest to move forward with a Tripal Hackathon/Meeting before PAG: specifically on Thursday, January 12 (Hackathon) and Friday, January 13 (Meeting)! As far as tentative agenda goes, we are planning on a round-table discussion similar to last year on Friday morning (8-12) with continued discussion open to other ideas (demo, hackathon, etc.) in the afternoon. As far as Thursday goes, it looks like there is interest in a hackathon-type meeting. We would love to get people from all experience levels together and are considering ideas such as helping each other make existing code sharable and implementing common download formats using the Tripal Download API. If you can make it to either the meeting or Hackathon we would love to hear from you so we know how many people to plan for. Furthermore, if you have any ideas for hackathon topics, please pass them along! Thanks! ~Lacey ------------------------------------------------------ Lacey-Anne Sanderson Bioinformaticist Pulse Crop Breeding and Genetics Phone: (306) 966-3208<tel://966-3208> Email: lac...@sh...<mailto:lac...@sh...> Room 2C33 Agriculture Department of Plant Sciences University of Saskatchewan On October 11, 2016 at 9:53:16 AM, Kucheran, Lacey Sanderson (la...@ma...<mailto:la...@ma...>) wrote: Hi Everyone, We would like to hold a Tripal Hackathon and/or Meeting before PAG 2017 since last years was so productive and well received! :-) We would like input from you as to whether you would find a meeting and/or hackathon most productive, as well as, which days work best for you. Please fill out this doodle poll if you are interested! http://doodle.com/poll/qqkwm3x4zrsqqinz Note: We would love to see a mix of developers, users and people just getting started with Tripal and will determine content with that in mind (and based on who responds to the poll). Everyone is welcome! Thanks! ~Lacey ------------------------------------------------------ Lacey-Anne Sanderson Bioinformaticist Pulse Crop Breeding and Genetics Phone: (306) 966-3208<tel://966-3208> Email: lac...@sh...<mailto:lac...@sh...> Room 2C33 Agriculture Department of Plant Sciences University of Saskatchewan |
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From: Stephen F. <spf...@gm...> - 2016-12-01 21:44:40
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Hi All, Due to the high number of deadlines most of us face prior to the end of the year I thought it best to cancel our official Users' meeting that is scheduled for tomorrow. We will have a great opportunity to meet in person for those attending the Tripal Hackathon/User's Meeting on Thursday and Friday prior to the Plant and Animal Genome (PAG) in San Diego. That meeting will substitute for our January User's meeting, although we may not be able to support call-ins... we'll see what we can do for that. More information about that meeting should follow soon. In our meeting last month I mistakenly said that this month's Tripal Meeting would be Dec 9th, but according to our schedule the first Friday of the month is tomorrow! If anyone has a particular topic of interest to discuss we could have an unofficial meeting next Friday, Dec 9th at the usual time to chat. If you would be interested in this let me know and I'll arrange the meeting. Regards, Stephen |
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From: Guignon, V. (Bioversity-France) <v.g...@cg...> - 2016-11-09 13:47:29
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The git command to use to download the module is: git clone --branch 7.x-1.x https://git.drupal.org/sandbox/guignonv/2429515.git tripal_mc If you used the previous instruction, then just rename the module directory: mv tripal_multi_chado tripal_mc Sorry for the inconvenience, Valentin Guignon From: Guignon, Valentin (Bioversity-France) [mailto:v.g...@cg...] Sent: mercredi 9 novembre 2016 12:10 To: gmo...@li... Subject: [Gmod-tripal-devel] Multi-Chado RC2 Hi! Here is an update on the Tripal Multi-Chado extension status: https://www.drupal.org/sandbox/guignonv/2429515 The module is now stable enough to be tested and used by the community. However, it currently requires the last *dev* version of Tripal 2 (released after November 1st, not tested on Tripal 3) and hopefully, it should be compatible with next Tripal 2.1 release. I updated the README.md file to reflect the last changes and to describe how to setup the thing according to your use-cases. Please feel free to review the module and give me some feedback. There is an issue queue (https://www.drupal.org/project/issues/2429515?categories=All) you can use for feature requests, bug reports and support. Currently, to get the module, you need to clone the git rep: git clone --branch 7.x-1.x https://git.drupal.org/sandbox/guignonv/2429515.git tripal_multi_chado However, I submitted a request to promote this module as an official Drupal extension: https://www.drupal.org/node/2825986 If you can review the module there (https://groups.drupal.org/node/427683) and help in the "promotion" process, the module will be sooner (or later) released as an official extension. I appreciate your time, Valentin Guignon |
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From: Guignon, V. (Bioversity-France) <v.g...@cg...> - 2016-11-09 11:10:25
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Hi! Here is an update on the Tripal Multi-Chado extension status: https://www.drupal.org/sandbox/guignonv/2429515 The module is now stable enough to be tested and used by the community. However, it currently requires the last *dev* version of Tripal 2 (released after November 1st, not tested on Tripal 3) and hopefully, it should be compatible with next Tripal 2.1 release. I updated the README.md file to reflect the last changes and to describe how to setup the thing according to your use-cases. Please feel free to review the module and give me some feedback. There is an issue queue (https://www.drupal.org/project/issues/2429515?categories=All) you can use for feature requests, bug reports and support. Currently, to get the module, you need to clone the git rep: git clone --branch 7.x-1.x https://git.drupal.org/sandbox/guignonv/2429515.git tripal_multi_chado However, I submitted a request to promote this module as an official Drupal extension: https://www.drupal.org/node/2825986 If you can review the module there (https://groups.drupal.org/node/427683) and help in the "promotion" process, the module will be sooner (or later) released as an official extension. I appreciate your time, Valentin Guignon |
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From: Stephen F. <spf...@gm...> - 2016-11-02 16:42:36
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Dear Tripal Developers and Users, We will have our monthly Online Tripal Developer and User meeting this Friday, Nov 4th. The meeting is open for everyone. If you have not previously attended, please consider attending especially if you are considering development of custom extensions. The goal of the meeting is to share news about Tripal, provide an opportunity to share ideas, ask questions, provide training, and to advertise what you are doing. This Friday is our "open mic" meeting. Where anyone can add items to the agenda. You can find an editable agenda at this link: https://docs.google.com/document/d/1qXriPRZeEpF9SqZdVhyIpsTbVyVLGrHJqYEsj13EyoA/edit?usp=sharing Depending on the list of agenda items we get, we may have a "round table" discussion to let folks discuss the project they're working on. The meeting start time and connection details follow below. See you there! Stephen *Meeting Start Time* Location Local time Time zone UTC offset Paris <https://www.timeanddate.com/worldclock/france/paris> (France - Île-de-France) Friday, November 4, 2016 at 4:00:00 PM CET <https://www.timeanddate.com/time/zones/cet> UTC+1 hour New York <https://www.timeanddate.com/worldclock/usa/new-york> (USA - New York) Friday, November 4, 2016 at 11:00:00 AM EDT <https://www.timeanddate.com/time/zones/edt> UTC-4 hours Des Moines <https://www.timeanddate.com/worldclock/usa/des-moines> (USA - Iowa) Friday, November 4, 2016 at 10:00:00 AM CDT <https://www.timeanddate.com/time/zones/cdt> UTC-5 hours Regina <https://www.timeanddate.com/worldclock/canada/regina> (Canada - Saskatchewan) Friday, November 4, 2016 at 9:00:00 AM CST <https://www.timeanddate.com/time/zones/cst> UTC-6 hours Los Angeles <https://www.timeanddate.com/worldclock/usa/los-angeles> (USA - California) Friday, November 4, 2016 at 8:00:00 AM PDT <https://www.timeanddate.com/time/zones/pdt> UTC-7 hours Beijing <https://www.timeanddate.com/worldclock/china/beijing> (China - Beijing Municipality) Friday, November 4, 2016 at 11:00:00 PM CST <https://www.timeanddate.com/time/zones/cst-china> UTC+8 hours Corresponding UTC (GMT) Friday, November 4, 2016 at 15:00:00 <https://www.timeanddate.com/worldclock/fixedtime.html?iso=20161104T1500> *Connection Details* Please join my meeting from your computer, tablet or smartphone. https://global.gotomeeting.com/join/762905221 You can also dial in using your phone. United States +1 (312) 757-3121 Access Code: 762-905-221 First GoToMeeting? Try a test session: http://help.citrix.com/getready <http://help.citrix.com/getready> |
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From: Kucheran, L. S. <la...@ma...> - 2016-10-26 20:01:41
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Quick Clarification:
You only need to update Tripal Blast, NOT all of Tripal. The update will not cause any interuptions on your site and all previously submitted jobs will be run normally.
Update by running
drush pm-update tripal_blast
on the command-line and then check [yoursite]/admin/reports/updates to ensure that Tripal BLAST is at version 7.x-1.2
~Lacey
------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-3208<tel://966-3208>
Email: lac...@sh...<mailto:lac...@sh...>
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan
On October 26, 2016 at 1:46:08 PM, Kucheran, Lacey Sanderson (la...@ma...<mailto:la...@ma...>) wrote:
Hi Everyone,
If you are using Tripal BLAST UI, be advised that a security release was made available today. Please update your Tripal sites ASAP!
This can be done using drush:
drush pm-update tripal_blast
Security Release:
View online: https://www.drupal.org/node/2822366
* Advisory ID: DRUPAL-SA-CONTRIB-2016-054
* Project: Tripal BLAST UI [1] (third-party module)
* Version: 7.x
* Date: 2016-October-26
* Security risk: 20/25 ( Highly Critical)
AC:Basic/A:None/CI:All/II:All/E:Theoretical/TD:All [2]
* Vulnerability: Remote code execution
———— DESCRIPTION ————
This module enables you to run NCBI BLAST jobs on the host system.
The module doesn't sufficiently validate advanced options available to users
submitting BLAST jobs, thereby exposing the ability to enter a short snippet
of shell code that will be executed when the BLAST job is run.
This vulnerability only requires the attacker to have minimal permissions on
the site (for example, "View published content") and therefore can be
exploited by untrusted or unauthenticated users in most cases.
~Lacey
------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-3208<tel://966-3208>
Email: lac...@sh...<mailto:lac...@sh...>
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan
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From: Kucheran, L. S. <la...@ma...> - 2016-10-26 19:46:15
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Hi Everyone,
If you are using Tripal BLAST UI, be advised that a security release was made available today. Please update your Tripal sites ASAP!
This can be done using drush:
drush pm-update tripal_blast
Security Release:
View online: https://www.drupal.org/node/2822366
* Advisory ID: DRUPAL-SA-CONTRIB-2016-054
* Project: Tripal BLAST UI [1] (third-party module)
* Version: 7.x
* Date: 2016-October-26
* Security risk: 20/25 ( Highly Critical)
AC:Basic/A:None/CI:All/II:All/E:Theoretical/TD:All [2]
* Vulnerability: Remote code execution
———— DESCRIPTION ————
This module enables you to run NCBI BLAST jobs on the host system.
The module doesn't sufficiently validate advanced options available to users
submitting BLAST jobs, thereby exposing the ability to enter a short snippet
of shell code that will be executed when the BLAST job is run.
This vulnerability only requires the attacker to have minimal permissions on
the site (for example, "View published content") and therefore can be
exploited by untrusted or unauthenticated users in most cases.
~Lacey
------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-3208<tel://966-3208>
Email: lac...@sh...<mailto:lac...@sh...>
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan
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From: Kucheran, L. S. <la...@ma...> - 2016-10-25 17:43:32
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Hi Everyone, I’m excited to say there is enough interest to move forward with a Tripal Hackathon/Meeting before PAG: specifically on Thursday, January 12 (Hackathon) and Friday, January 13 (Meeting)! As far as tentative agenda goes, we are planning on a round-table discussion similar to last year on Friday morning (8-12) with continued discussion open to other ideas (demo, hackathon, etc.) in the afternoon. As far as Thursday goes, it looks like there is interest in a hackathon-type meeting. We would love to get people from all experience levels together and are considering ideas such as helping each other make existing code sharable and implementing common download formats using the Tripal Download API. If you can make it to either the meeting or Hackathon we would love to hear from you so we know how many people to plan for. Furthermore, if you have any ideas for hackathon topics, please pass them along! Thanks! ~Lacey ------------------------------------------------------ Lacey-Anne Sanderson Bioinformaticist Pulse Crop Breeding and Genetics Phone: (306) 966-3208<tel://966-3208> Email: lac...@sh...<mailto:lac...@sh...> Room 2C33 Agriculture Department of Plant Sciences University of Saskatchewan On October 11, 2016 at 9:53:16 AM, Kucheran, Lacey Sanderson (la...@ma...<mailto:la...@ma...>) wrote: Hi Everyone, We would like to hold a Tripal Hackathon and/or Meeting before PAG 2017 since last years was so productive and well received! :-) We would like input from you as to whether you would find a meeting and/or hackathon most productive, as well as, which days work best for you. Please fill out this doodle poll if you are interested! http://doodle.com/poll/qqkwm3x4zrsqqinz Note: We would love to see a mix of developers, users and people just getting started with Tripal and will determine content with that in mind (and based on who responds to the poll). Everyone is welcome! Thanks! ~Lacey ------------------------------------------------------ Lacey-Anne Sanderson Bioinformaticist Pulse Crop Breeding and Genetics Phone: (306) 966-3208<tel://966-3208> Email: lac...@sh...<mailto:lac...@sh...> Room 2C33 Agriculture Department of Plant Sciences University of Saskatchewan |
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From: Kucheran, L. S. <la...@ma...> - 2016-10-11 15:53:23
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Hi Everyone, We would like to hold a Tripal Hackathon and/or Meeting before PAG 2017 since last years was so productive and well received! :-) We would like input from you as to whether you would find a meeting and/or hackathon most productive, as well as, which days work best for you. Please fill out this doodle poll if you are interested! http://doodle.com/poll/qqkwm3x4zrsqqinz Note: We would love to see a mix of developers, users and people just getting started with Tripal and will determine content with that in mind (and based on who responds to the poll). Everyone is welcome! Thanks! ~Lacey ------------------------------------------------------ Lacey-Anne Sanderson Bioinformaticist Pulse Crop Breeding and Genetics Phone: (306) 966-3208<tel://966-3208> Email: lac...@sh...<mailto:lac...@sh...> Room 2C33 Agriculture Department of Plant Sciences University of Saskatchewan |
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From: Stephen F. <spf...@gm...> - 2016-10-05 22:38:20
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Dear Tripal Developers and Users, We will have our monthly Tripal Developer and User meeting this Friday, Oct 7th. The meeting is open for everyone. If you have not previously attended, please consider attending especially if you are considering development of custom extensions. The goal of the meeting is to share news about Tripal, provide an opportunity to share ideas, ask questions, provide training, and to advertise what you are doing. The meeting start time and connection details follow below. The meeting agenda is currently blank. I will add to it before the meeting Friday but if you have something you'd like to discuss please add it (include your name): https://docs.google.com/document/d/1niPq48OAS1l3_ErIZkQxpDE4yEImaz0uLZS_Tl2GZic/edit# Chat soon! Stephen UTC: 3pm European Central (GMT+2): 5pm US Eastern (GMT-4): 11 am US Central (GMT-5): 10 am Canada Regina (GMT-6): 9 am US Pacific (GMT-7): 8 am China (GMT+8): 11 pm *Connection Details: * Please join my meeting from your computer, tablet or smartphone. https://global.gotomeeting.com/join/185724269 You can also dial in using your phone. United States +1 (408) 650-3123 Access Code: 185-724-269 |
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From: Stephen F. <spf...@gm...> - 2016-09-12 17:41:49
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Hi All, Thanks to those who participated in the poll! From our Doodle poll it looks like our Tripal User's Meeting is best on the 1st Friday of the month. Because we've already passed that day for this month it looks like our next meeting will be on Friday October 7th at 3pm UTC (4pm European Central/11am US Eastern/ 10 am Regina Canada / 10 am US Central / 8am US Pacific). If we keep to our schedule this next meeting should be a training meeting. I've created an agenda document. If there are specific areas you would like to see training can you click the link below and add any suggestions: https://docs.google.com/document/d/1niPq48OAS1l3_ErIZkQxpDE4yEImaz0uLZS_Tl2GZic/edit?usp=sharing Due to business in August we skipped our monthly meeting and if we wait until Oct 7th that is about 2 months of no verbal interaction. If anyone is interested to meet and chat on specific issues it seemed the next best day was the 3rd Friday. So, we could have a less formal meeting this Friday, Sept 16th if there is interest. Please let me know. Stephen |
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From: Scott C. <sc...@sc...> - 2016-09-02 15:05:49
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I think there a probably some people (besides me) using stag-storenode, but probably not many. The majority of Chado users these days are using Tripal, so we'd want to see the current Tripal ontology loader updated as well. I cc'ed the dev list to make sure they're aware of it too (though I imagine they're all on the Chado list too). On Fri, Sep 2, 2016 at 7:38 AM, Chris Mungall <cjm...@lb...> wrote: > > For a while there has been a need of a developer-friendly replacement > for OBO format. While advanced applications should target OWL, there a > number of things that make direct OWL consumption developer-unfriendly > (especially perl and python developers) > > We have come up with a proposed JSON representation that is intended to > have the simplicity of OBO, with optional extensions for advanced OWL > axioms - in JSON or YAML: > https://github.com/geneontology/obographs > > The intent is for any replacements for stage-storenode.pl to target this > (I'm not up to date on what people are currently using) > > It shouldn't be regarded as stable yet - I'd like feedback from the GMOD > community first. Please email here or use the issue tracker with any > comments, thanks! > > ------------------------------------------------------------ > ------------------ > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
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