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From: Shawna Sp <sha...@gm...> - 2018-04-19 14:39:05
|
Hi all, This Friday we will have two help desk meetings. Here is the info: *11:00 am PST | Noon MDT | 2:00 pm EST* Integrating Tripal Collections with the Drupal Search API *Meeting info:* https://zoom.us/j/471551977 Or iPhone one-tap : US: +16699006833,,471551977# or +14087403766,,471551977# Or Telephone: Dial(for higher quality, dial a number based on your current location): US: +1 669 900 6833 or +1 408 740 3766 or +1 646 876 9923. Meeting ID: 471 551 977. International numbers available: https://zoom.us/u/bFbwpVK3B *Noon PST | 1:00 pm MDT | 3:00 pm EST* tripal_phylotree extension module discussion *Meeting info:* https://zoom.us/j/478593389 Or iPhone one-tap: US: +16468769923,,478593389# or +16699006833,,478593389# Or Telephone: Dial(for higher quality, dial a number based on your current location): US: +1 646 876 9923 or +1 669 900 6833 or +1 408 740 3766. Meeting ID: 478 593 389. International numbers available: https://zoom.us/u/ea7qDrSlW See you then! |
From: Shawna Sp <sha...@gm...> - 2018-04-17 21:10:53
|
Hi all, Just a quick reminder, if you have anything you need help on or would like to discuss please fill out this form as soon as possible (and no later than first thing tomorrow, 4/18, morning): https://goo.gl/forms/v9kamkrP9UdOhS8j1 Thanks! |
From: Shawna Sp <sha...@gm...> - 2018-04-15 12:59:15
|
Hi all, This Friday, April 20, 2018, we will be running our second set of Tripal Help Desk virtual collaboration meetings. If you have a specific topic you need help with please fill out this google form by this Tuesday, April 17: https://goo.gl/forms/v9kamkrP9UdOhS8j1 Thanks! On Tue, Mar 27, 2018 at 11:32 AM, Shawna Sp <sha...@gm...> wrote: > Hi all, > > We will be running our second round of Tripal Help Desk virtual > collaboration meetings on Friday, April 20, 2018. > > As a reminder, the aim of these sessions is to match up people who need > help with people who can help. Once we have the times and topics worked > out we will post them on the tripal.info site, and email a list of > topics, times, and virtual room links to this mailing list. > > If you have a specific topic you need help with please fill out this > google form by Tuesday, April 17: > https://goo.gl/forms/v9kamkrP9UdOhS8j1 > > Thanks! > Shawna > |
From: Shawna Sp <sha...@gm...> - 2018-04-04 16:50:53
|
Hi all, We will be having our monthly Tripal user’s meeting this Friday, April 6 at 8 am PST / 11 am EST. You can find the specific time in your area via this link: https://www.timeanddate.com/worldclock/fixedtime.html?msg=Tripal+User%27s+Meeting+April+2018&iso=20180406T08&p1=2035&ah=1 *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=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=qWgkms0kw7fEr0PIBgw2aiBS4wnWF8UXXVopVbrms1Q&m=_F4kDE7x55n5m2hd1fLe276qCrEquEAvLqhy2BrtLGs&s=CCcppZj_6P-kgivFG2S8gAKUgiVXqpmP3T2A2hUM0dE&e=> You can also dial in using your phone. United States: +1 (312) 757-3121 <(312)%20757-3121> Access Code: 762-905-221 Thanks! |
From: Scott C. <sc...@sc...> - 2018-04-02 16:08:57
|
---------- Forwarded message ---------- From: Iddo Friedberg <id...@gm...> Date: Mon, Apr 2, 2018 at 10:19 AM Subject: [isb-biocuration] Function @ISMB 2018: Abstract Deadline this week To: isb...@go... Call for Abstracts: Function Special Interest Group at ISMB 2018 We call upon all researchers involved in the computational study of macromolecular function to submit an abstract to the Function-SIG meeting. Authors of selected abstracts will be invited to give a talk and/or present a poster. Travel fellowships will be available for qualifying graduate students and postdoctoral trainees. Time and place: Chicago, IL, USA July 6, 2018 ISMB 2018 home page: https://www.iscb.org/ismb2018 Key Dates: *Thursday April 5, 2018* Abstract Submission Deadline *April 26, 2018*: Notification of Acceptance *July 7, 2018*: Function SIG at ISMB/ECCB 2018 Abstract submission: http://biofunctionprediction.org/content/submit-abstract Sequence and structure genomics have generated a wealth of data, but extracting meaningful information from genomic data is challenging. Both the number and the diversity of discovered sequences are increasing. In addition, there is a need for standardized annotation that could be incorporated into functional annotation on a large scale. Finally, there is a need to assess the quality of the function prediction algorithms and software. For these reasons and many more, automated protein function prediction is of interest to computational biologists in academia and industry. The Function-SIG meetings offer researchers and students in the field to meet with like-minded colleagues, learn about the latest developments in the field, and forge new collaborations. More on the Function SIG: http://biofu nctionprediction.org/ We will also present the more results from the third round of the Critical Assessment of Functional Annotation (CAFA3) and from the additional CAFA3.14 (CAF-Pi). CAFA is an international computational challenge funded by the NSF and BBSRC which aims to asses the accuracy of protein function prediction methods which is drawing dozens of participating groups worldwide. More on CAFA: http://biofunctionprediction.org/cafa/ -- Iddo Friedberg http://iddo-friedberg.net/contact.html ++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.> ++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----. .>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>> >>----.<--.>++++++.<<<<------------------------------------. -- You received this message because you are subscribed to the Google Groups "International Society for Biocuration" group. To unsubscribe from this group and stop receiving emails from it, send an email to isb...@go.... To post to this group, send email to isb...@go.... To view this discussion on the web visit https://groups.google.com/d/ msgid/isb-biocuration/CABm4-MRzXiWia5Ud7eVAXO63KyCz0xL8yvA QeUZPOQQ4Yafaaw%40mail.gmail.com <https://groups.google.com/d/msgid/isb-biocuration/CABm4-MRzXiWia5Ud7eVAXO63KyCz0xL8yvAQeUZPOQQ4Yafaaw%40mail.gmail.com?utm_medium=email&utm_source=footer> . For more options, visit https://groups.google.com/d/optout. -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Sanders, S. <ss...@iu...> - 2018-03-30 18:15:01
|
Hey all, NCGAS has a new service - Pop Up Genome Browsers with some custom tools! This is now a public Jetstream Image?<https://use.jetstream-cloud.org/application/images/657>. Once you spin it up, you can simply go to your URL and access a premade site. The documentation will walk you through how to: * add your own JBrowse reference and tracks (THROUGH A GUI!!) * make your own BLAST databases (THROUGH A GUI) that are linked to the jbrowse so you can visualize your results instantly! * how to customize your site from there! How to get access: 1) If you are a genomics researcher or field station researcher - email me your XSEDE account name and see Getting Started on Jetstream?<http://ncgas.org/Blog_Posts/Getting%20Started%20on%20Jetstream.php>. I will add you to one of our allocations (depending your group!) and then you can get into Jetstream, spin up a browser and roll! 1b) If you are not, but are a researcher at a US institution, you can request your own allocation start up - feel free to email me on details of how to do this - I have canned instructions that help with what to request, etc. 2) While you wait to be added, feel free to check out the documentation and demo site here<http://ncgas.org/WelcomeBasket_PopUpBrowser.php>! Feel free to send me any questions/comments/suggestions! Have fun! Sheri Sanders Bioinformatic Analyst National Center for Genome Analysis and Support (NCGAS) NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center. |
From: Stephen F. <spf...@gm...> - 2018-03-29 02:34:05
|
Hi Folks, In case you were not aware there is a very important Drupal security fix. Please consider updating your sites! Follow this link for details: https://www.drupal.org/sa-core-2018-002 Stephen |
From: Shawna Sp <sha...@gm...> - 2018-03-27 15:33:05
|
Hi all, We will be running our second round of Tripal Help Desk virtual collaboration meetings on Friday, April 20, 2018. As a reminder, the aim of these sessions is to match up people who need help with people who can help. Once we have the times and topics worked out we will post them on the tripal.info site, and email a list of topics, times, and virtual room links to this mailing list. If you have a specific topic you need help with please fill out this google form by Tuesday, April 17: https://goo.gl/forms/v9kamkrP9UdOhS8j1 Thanks! Shawna |
From: Stephen F. <spf...@gm...> - 2018-03-14 20:02:55
|
Hi All, Just a correction, on the time. The invite below accidentally lists two different times. The meeting is at 8am Pacific Time US and 11am Eastern Time US, plus whatever timezone where you are located as per the link. Sorry for any confusion. Stephen On 3/14/2018 9:24 AM, Stephen Ficklin wrote: > Dear Tripal Community. > > This Friday we will have our next training event. The topic will be > step-by-step instructions for creation of Tripal Fields which is the > new method in Tripal v3 for creation of custom content. Tripal Fields > provide more flexibility than the template files of Tripal v2 but > require more planning. The meeting is at 8am Pacific US time, 4pm UTC. > > You can find the specific time in your area here: > > https://www.timeanddate.com/worldclock/fixedtime.html?msg=Tripal+Fields+Training+Event&iso=20180316T08&p1=2035&ah=2 > > > Meeting connection details are below. > > Hope to see you there! > > Stephen > > Connection details for the meeting are below: > > Topic: Tripal Training > Time: Mar 16, 2018 8:00 AM Eastern Time (US and Canada) > > Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/206865336 > > Or iPhone one-tap : > US: +14087403766,,206865336# or +16468769923,,206865336# > Or Telephone: > Dial(for higher quality, dial a number based on your current > location): > US: +1 408 740 3766 or +1 646 876 9923 or +1 669 900 6833 > Meeting ID: 206 865 336 > International numbers available: > https://zoom.us/zoomconference?m=TWZq5WhKISFqX08d6eUVlMc1DfDdiahD > > |
From: Stephen F. <spf...@gm...> - 2018-03-14 16:24:29
|
Dear Tripal Community. This Friday we will have our next training event. The topic will be step-by-step instructions for creation of Tripal Fields which is the new method in Tripal v3 for creation of custom content. Tripal Fields provide more flexibility than the template files of Tripal v2 but require more planning. The meeting is at 8am Pacific US time, 4pm UTC. You can find the specific time in your area here: https://www.timeanddate.com/worldclock/fixedtime.html?msg=Tripal+Fields+Training+Event&iso=20180316T08&p1=2035&ah=2 Meeting connection details are below. Hope to see you there! Stephen Connection details for the meeting are below: Topic: Tripal Training Time: Mar 16, 2018 8:00 AM Eastern Time (US and Canada) Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/206865336 Or iPhone one-tap : US: +14087403766,,206865336# or +16468769923,,206865336# Or Telephone: Dial(for higher quality, dial a number based on your current location): US: +1 408 740 3766 or +1 646 876 9923 or +1 669 900 6833 Meeting ID: 206 865 336 International numbers available: https://zoom.us/zoomconference?m=TWZq5WhKISFqX08d6eUVlMc1DfDdiahD |
From: Allyson L. <all...@oe...> - 2018-03-04 08:25:46
|
Dear Database developers, I'm contacting you on behalf of FAIRsharing (https://fairsharing.org/, http://dx.doi.org/10.1093/database/baw075), an online registry of scientific data standards, databases and policies. Our aim is to make your resource as visible as possible to as large an audience as possible. Bradford Condon recently created a collection for databases implementing Tripal (https://fairsharing.org/collection/Tripal). In addition to his work, I have added or curated FAIRsharing database records for all 17 of the resources listed on tripal.info. You will find links to these records below: - Banana Genome Hub - https://fairsharing.org/FAIRsharing.p90p8q - Cacao Genome Database - https://fairsharing.org/biodbcore-001054 - Citrus Genome Database - https://fairsharing.org/bsg-d001053 - Cool Season Food Legume Genome Database - https://fairsharing.org/biodbcore-001055 <https://fairsharing.org/biodbcore-001055> - CottonGen - https://fairsharing.org/biodbcore-001056 - Genome Database for Rosaceae - https://fairsharing.org/FAIRsharing.6v96ma - Genome Database for Vaccinium - https://fairsharing.org/ biodbcore-001060 - Hardwood Genomics Project - https://fairsharing.org/FAIRsharing.srgkaf - Cucurbit Genomics Database - https://fairsharing.org/biodbcore-001057 - GeneNet Engine - https://fairsharing.org/biodbcore-001059 - i5k Workspace@NAL - https://fairsharing.org/biodbcore-001050 - KnowPulse - https://fairsharing.org/biodbcore-001061 - LIS - https://fairsharing.org/biodbcore-001062 - MTGD - https://fairsharing.org/biodbcore-001063 - Musa Germplasm Information System - https://fairsharing.org/FAIRsharing.kthr0s - PeanutBase - https://fairsharing.org/biodbcore-001064 - Planosphere - https://fairsharing.org/biodbcore-001065 (Together with its sister resource, the Planarian Anatomy Ontology at https://fairsharing.org/bsg-s000987 <https://fairsharing.org/bsg-s000987> ) Bradford and I have communicated via email, and he suggested I contact this mailing list. To ensure our information is as correct and up to date as possible, would you or someone from your teams please claim any that your groups maintain directly? You can claim each record (for those resources you directly maintain) via their "Claim Ownership" buttons. Claiming a record as either a group or an individual also gives you the opportunity to make changes to the record yourself, allowing you complete control over how your resource is displayed in FAIRsharing. In addition, if you claim a record(s) as an individual, you can link the record to your ORCID. FAIRsharing is about making your resource discoverable to a variety of users, such as journals and publishers, researchers and service providers, research and infrastructure projects and programmes, as well as curators, librarians, funders and other policy makers and data scientists ( https://fairsharing.org/communities). A claimed record helps users find up-to-date information and contacts should they have any questions about your resource. Regards, Allyson -- Dr. Allyson Lister Knowledge Engineer, FAIRsharing & ISA-Tools University of Oxford e-Research Centre http://www.fairsharing.org/communities http://www.isa-tools.org/person/allyson-lister/ ORCiD: 0000-0002-7702-4495 Twitter: @allysonlister http://themindwobbles.wordpress.com Please note that I work part time, mainly Tuesdays, Wednesdays and Thursdays. If the matter is urgent, you may wish to email co...@fa... instead. |
From: Stephen F. <spf...@gm...> - 2018-02-28 18:49:31
|
Hi All, It seems Sourceforge accidentally sent the email below a second time. We're a bit baffled by it. Please disregard. We do however have our regularly scheduled Tripal User's Meeting this Friday as per the email Shawna sent earlier this week. Apologies for any confusion. Stephen On Tue, Feb 20, 2018 at 2:11 PM, Shawna Sp <sha...@gm...> wrote: > Hi all, > > This Friday, February 23, we will be running our first Tripal Help Desk > virtual collaboration meetings. > > If you have questions or topics you'd like to work on please fill out > this google form by end of day tomorrow, February 21: > https://goo.gl/forms/abA4DJR3hQmnj7jw1 > > Thanks! > Shawna > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gmod-tripal mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-tripal > > |
From: Shawna Sp <sha...@gm...> - 2018-02-28 04:04:35
|
Hi all, This Friday, February 23, we will be running our first Tripal Help Desk virtual collaboration meetings. If you have questions or topics you'd like to work on please fill out this google form by end of day tomorrow, February 21: https://goo.gl/forms/ abA4DJR3hQmnj7jw1 Thanks! Shawna |
From: Scott C. <sc...@sc...> - 2018-02-23 17:57:03
|
*GCCBOSC 2018: A Bioinformatics Community Conference* *Call for Abstracts * * Dates*: June 25-30, 2018 * Location*: Reed College, Portland, OR * GCCBOSC website*: https://gccbosc2018.sched.com/ * BOSC website: *https://www.open-bio.org/wiki/BOSC_2018 * Email BOSC organizers*: b <bo...@op...>os...@op... * BOSC announcements mailing list*: http://lists.open-bio. org/mailman/listinfo/bosc-announce * Twitter*: @OBF_BOSC <https://twitter.com/OBF_BOSC>, #GCCBOSC *Important Dates* - *Abstract submission <https://www.open-bio.org/wiki/BOSC_Abstract_Submission> deadline: March 16, 2018* - Authors notified: April 10, 2018 - Travel fellowship <https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md> application deadline: April 15, 2017 - GCCBOSC 2018 Training: June 25-26, 2018 - GCCBOSC 2018 Talks: June 27-28 - GCCBOSC CollaborationFest: June 29-30 *About BOSC* Since 2000, the yearly Bioinformatics Open Source Conference (BOSC) has provided a forum for developers and users to interact and share research results and ideas in open source bioinformatics. BOSC’s broad spectrum of topics includes practical techniques for solving bioinformatics problems; software development practices; standards and ontologies; approaches that promote open science and sharing of data, results and software; and ways to grow open source communities while promoting diversity within them. *Why is BOSC partnering with GCC in 2018?* In past years, BOSC has been part of the ISMB conference. Because of our continuing focus on broadening and deepening the BOSC community, we've been exploring ways to reach those in the bioinformatics community who aren’t already part of the audience attracted by ISMB. As part of that exploration, we have looked at other organizations and conferences that have been successful at establishing a strong and growing community of participants, such as the Galaxy Community Conference (GCC). After much discussion and planning, we decided to hold BOSC in conjunction with GCC in 2018. We hope that this will be an enjoyable and productive experience for all participants, and we welcome your feedback before, during and after the event. As always, BOSC 2018 will include two days of talks and posters, two keynote speakers <https://galaxyproject.org/events/gccbosc2018/keynotes/>, a panel discussion, Birds of a Feather, and more. BOSC sessions will run in parallel with GCC 2018 sessions, with some sessions shared. The two days of talks will be preceded by two days of training <https://galaxyproject.org/events/gccbosc2018/training/> on topics nominated by the community, and will be followed by a two-day CollaborationFest that merges BOSC's Codefest and Galaxy's Developer and User Hackathon Days. *Abstract submission* We encourage you to submit one-page abstracts (due March 16) on any topic relevant to open source bioinformatics or open science. After review, some abstracts will be selected for lightning talks, longer talks, demos and/or posters. Abstract submission instructions and a link to the EasyChair submission portal can be found on https://www.open-bio.org/ wiki/BOSC_Abstract_Submission *BOSC session topics include* (but are not limited to): - Open Science and Reproducible Research - Open Biomedical Data - Citizen/Participatory Science - Standards and Interoperability - Data Science - Workflows - Visualization - Medical and Translational Bioinformatics - Developer Tools and Libraries - Bioinformatics Open Source Project Progress Reports We look forward to receiving your abstract and meeting you at GCCBOSC 2018! Sincerely, BOSC 2018 Organizing Committee: Nomi Harris (chair), Heather Wiencko (co-chair), Brad Chapman (co-chair), Peter Cock, Christopher Fields, Bastian Greshake, Karsten Hokamp, Hilmar Lapp, Monica Munoz-Torres P.S. Don't forget to submit your BOSC abstract by March 16 at https://www.open-bio.org/wiki/BOSC_Abstract_Submission! Please share this announcement with your colleagues! -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Shawna Sp <sha...@gm...> - 2018-02-22 18:32:08
|
Hi All, Below please find the subject, scheduled time, and links for each of the 3 Tripal Help Desk meetings we will be having tomorrow, Friday, February 23, 2018. *Subject: Tripal v2 to v3 upgrade issues * Time: 9 am PST, 10 am Mountain Time, 12 pm EST Link: https://zoom.us/j/856350863 <https://www.google.com/url?q=https%3A%2F%2Fzoom.us%2Fj%2F856350863&sa=D&usd=2&usg=AFQjCNHRWJA1XguQ1pDd8z_urR-A_-KP9w> ______________________ *Subject: Web Services* Time: 10:30 am PST, 11:30 am Mountain Time, 1:30 pm EST Link: https://zoom.us/j/113272308 <https://www.google.com/url?q=https%3A%2F%2Fzoom.us%2Fj%2F113272308&sa=D&usd=2&usg=AFQjCNH1RScB-ypebI-pNAq2rvIelskzjA> ______________________ *Subject: Ontology Load issues (Sequence Ontology)* Time: 12 pm PST, 1 pm Mountain Time, 3 pm EST Link: https://zoom.us/j/353807676 <https://www.google.com/url?q=https%3A%2F%2Fzoom.us%2Fj%2F353807676&sa=D&usd=2&usg=AFQjCNErVD6tFvHYpI6bN1hbEiL2-WnB1w> Feel free to join any meeting that may be of interest to you or that you might have insight into. Thanks, Shawna |
From: Shawna Sp <sha...@gm...> - 2018-02-16 14:22:01
|
Hi all, We will be running our first Tripal Help Desk virtual collaboration meetings on Friday, February 23, 2018. Due to scheduling conflicts, we will be having this first meeting on the 4th Friday of the month but after this, we will switch to the 3rd Friday of the month. The aim of these sessions is to match up people who need help with people who can help. We'll be grouping issues together like if there are several groups who need to work on Tripal Fields we'll put them in the same session. Once we have the times and topics worked out we will post them on the tripal.info site, and email a list of topics, times, and virtual room links to this mailing list so you can join in on sessions that might be useful to you even if you didn't submit a specific issue. If you'd like to participate please fill out this google form by Wednesday, February 21: https://goo.gl/forms/abA4DJR3hQmnj7jw1 Thanks! Shawna |
From: Stephen F. <spf...@gm...> - 2018-02-07 18:13:35
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Hello! We'd like to gauge interest in having a Tripal training workshop during or before the Plant biology meeting in Montreal, Canada (https://aspb.org/event/plant-biology-2018/). I have put together a simple poll to gauge interest. It should take less than 1 minute to fill out: https://doodle.com/poll/z3zbfsadgsyqbu3d Even if you are not planning to attend the conference we'd appreciate if you could take the poll and indicate that as well. Also, there is a comment section on the poll if you feel inclined to comment on such an event. Thanks, Stephen |
From: Sook J. <so...@gm...> - 2018-02-02 21:41:01
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Hello, Since there is a discussion whether or not to use nd_module for storing phenotype and genotype data in Chado, we wanted to share what we do at GDR, CottonGEN and our other databases. Using the nd_experiment table to link stock and genotype (and project, etc) gave us (and others) a severe performance issue. Lacey came up with the idea of using genotype_call table to link genotype and stock (and project etc). https://github.com/UofS-Pulse-Binfo/nd_genotypes/wiki/How-to-Store-your-Data We adopted this and it has been working very well. We decided to make a similar table to link stock and phenotype tables as well for large-scale phenotype data. We have BIMS Tripal module, which breeders use to store/manage their private data and we anticipate the users (so their data) will grow extensively. Some of them will have phenomics data and the volume of phenotype data will become extensive. The phenotype_call table we create is as follows. phenotype_call_id INT PK phenotype_id INT FK project_id INT FK stock_id INT FK nd_geolocation_id INT FK time TIMESTAMP WITHOUT TIMEZONE This table is basically to link the 'sample' stored in stock table (a specific tree or plot of plants that are being phenotyped) and specific phenotypic value stored in 'phenotype' table. Time field is needed here since the exact phenotyping time can be different for each phenotype for the same sample (this data comes from the FieldBook App that many breeders use). nd_location_id is added here since we don't go through nd_experiment and we need to store the location info of the plant (or animal/insect). I don't think this means that we can get rid of nd module. Nd_experiment table and other associated nd tables are being used for experiments using stocks other than phenotyping and genotyping. Examples are cross, field collection, etc. There are also databases that store various protocols and reagents that are associated with experiments (hence nd_protocol, nd_reagents, etc). For us we need nd_experiment table to store cross data and we don't have data for nd_protocol and nd_reagents. One of the important things that came out of ND discussions were using stock table to store 'samples' and use stock_relationship table to store stock and the sample. There were thoughts to create a separate table such as 'observation_unit' etc. The same principle goes with the project table and project_relationship table to store hierarchical datasets. I think we can think of genotype and phenotype as specific examples of 'experiment' that generate HUGE quantity of data so we use specific linker tables without going through the nd_experiment. It would be nice to open up the conversation to come up with consensus but temporarily we have to use these two tables to speed up loading of our data. Hope it helps! Thanks! Sook and Taein |
From: Meg S. <me...@gm...> - 2018-01-25 19:59:49
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Hello, We recently held a hackathon and user meeting in San Diego. Whether you attended or not, please consider taking this survey to give the organizers your feedback - there are different questions depending on if you were there or not. We'll be incorporating your answers into planning future events and appreciate your comments. https://utk.co1.qualtrics.com/jfe/form/SV_9tN0NUsNmv65Nat Apologies if you receive this email twice. Thanks for your time, Meg, Ethy and Stephen -- Margaret Staton Assistant Professor Department of Entomology and Plant Pathology 370 PBB, 2505 EJ Chapman Drive Knoxville, TN 37996-4560 864-506-4515 Mobile mst...@ut... |
From: Scott C. <sc...@sc...> - 2018-01-25 18:45:41
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Hi Olga, This is more of a Tripal question, so I'm cc'ing the Tripal list. Scott On Thu, Jan 25, 2018 at 7:33 AM, Olga Klonova <Olg...@st...> wrote: > Hi, > > I have a question about a creating a template for the bulk loader. I am > aware of the tutorial on tripal.org, which is absolutely useful, as well > as some posts on the list, but my file seems to be too large to be fit into > a Chado database using the steps from the tutorial. > > In the file each protein has multiple references to external databases > (UniProt, PDB, PFAM) and EC number, information about relevant genes (GI > number, GN, GO), the organism (Taxonomy ID, domain, class, family, genus, > species), and some fields for the protein itself (ID, description, sequence > length). All in all about 20 columns. > > Guess creating a template the usual way (as described in the tutorial) > would lead to a mess, as there are too many fields to use and cross-link. > So I wonder if there is a (recommended) way to load such data into Chado > more efficiently. Would long format help (instead of the wide format, which > is being used now)? Or is it better to split the data into several subsets > and load each independently? Or re-organise the columns somehow? > > Any help would be very much appreciated. > > Olga > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > 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 |
From: Meg S. <me...@gm...> - 2018-01-22 19:35:08
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Hi, The Galaxy Community Conference will be held in tandem with the Bioinformatics Open Source Community conference this summer in Portland, Oregon, United States, June 25-30, 2018. The meeting is kicking off with 2 days of training in open source bioinformatics tools. Stephen, Jill and I have proposed two Tripal training topics: "Building a Community Genome Database with Tripal v3" and "Adding Galaxy Workflows to a Tripal Website". If you think you would like to attend the conference or would like to attend the training, please vote for training topics here: http://bit.ly/gccbosc2018-vote Thanks! Meg ---------- Forwarded message ---------- From: Dave Clements <cle...@ga...> Date: Mon, Jan 22, 2018 at 2:07 PM Subject: [GMOD-devel] GCCBOSC 2018 Training Topic Voting is now open To: GMOD Developers List <gmo...@li...> Cc: GCCBOSC 2018 Organizers <gcc...@li...> Hello all, Voting is now open <http://bit.ly/gccbosc2018-vote> on what training topics <https://galaxyproject.org/events/gccbosc2018/training/> will be offered at GCCBOSC 2018 <https://gccbosc2018.sched.com/>. Your vote <http://bit.ly/gccbosc2018-vote> will determine the topics that are offered, which topics should be offered more than once, and which ones should not be scheduled at the same time. Your vote matters. *Topic voting closes January 31.* The Training schedule, including instructors, will be published before early registration opens. GCCBOSC2018 <https://gccbosc2018.sched.com/> will be held 25-30 June in Portland, Oregon, United States. It will feature two days of training: the second of which is multi-track and will feature content for both the BOSC and Galaxy communities. Workshops will be hands-on and participants will be strongly encouraged to bring a laptop and follow along. If you work in data-intensive biomedical research, there is no better place than GCCBOSC 2018 to present your work and to learn from others. Thanks, and see you in Portland! The GCCBOSC 2018 Organizers <https://galaxyproject.org/events/gccbosc2018/organizers> -- https://galaxyproject.org/ https://usegalaxy.org/ ------------------------------------------------------------ ------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Gmod-devel mailing list Gmo...@li... https://lists.sourceforge.net/lists/listinfo/gmod-devel -- Margaret Staton Assistant Professor Department of Entomology and Plant Pathology 370 PBB, 2505 EJ Chapman Drive Knoxville, TN 37996-4560 864-506-4515 <(864)%20506-4515> Mobile mst...@ut... |
From: Stephen F. <spf...@gm...> - 2018-01-22 19:03:35
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Hi All, As in year's past the GMOD group has been involved with the Google Summer of Code under the the organization called "Open Genome Informatics". See the email below forwarded from Marc. Google essentially funds a remote student to work on an open-source project of your choice. I participated two years ago and had a good experience with it. You can participate by contacting Marc Gillespie, Robin Haw or Scott Cain (emails below). You need a project idea for the student to work on over the summer. If you'd like to know more about how it went for me I'd be happy to answer any questions. I did find, though that because the summer goes by so fast, a Drupal-related task is probably not best because Drupal has a high learning curve. If you have some other work, such as visualization that can be done outside of Drupal then that might be more appropriate. Best, Stephen -------- Forwarded Message -------- Subject: Re: [GSoC 2018] [Open Genome Informatics] Google Summer of Code 2018 Participation Date: Fri, 19 Jan 2018 11:11:04 -0500 From: Marc Gillespie <gil...@gm...> To: Marc E Gillespie PhD <gil...@st...> CC: Robin Haw <Rob...@oi...>, Scott Cain <sc...@sc...> Hi All, With the approaching date we will nEed to hear from you shortly. Please let me know what your plans for participation are. I look forward to hearing from you! Marc Marc E. Gillespie Reactome biocurator reactome.org <http://reactome.org> On Jan 7, 2018, at 5:32 PM, Robin Haw <rob...@gm... <mailto:rob...@gm...>> wrote: > Dear All, > > The Open Genome Informatics team serves as an "umbrella organization" > to a variety of open bioinformatics projects, including GMOD and its > software projects -- GBrowse, JBrowse, etc.; Galaxy; Reactome; > SeqWare; WormBase; DockStore and others. I’ll update the Open Genome > Informatics page: http://gmod.org/wiki/GSoC, in preparation for > applying for this year’s Google Summer of Code. > > *_Call for 2018 Project Ideas and Mentors:_* We are seeking project > ideas to post and attract talented students to this year’s Summer of > Code competition. If you have a project idea for which you would like > to mentor a student, please contact *Marc Gillespie, Robin Haw and > Scott Cain (emails above).* > > _*Mentoring organization application deadline*_*_:__ 23rd January 2018._* > *_ > _* > Please forward this to others who might be interested in taking part. > * > * > If you have any questions please let Marc, Scott and I know. > > Thanks, > Robin Haw > |