- Galaxy-training - lists.galaxyproject.org

Fwd: Workshop "Using clouds and VMs in bioinformatics training", 23.-25.5 Finland
by Dave Clements 24 Mar '16

24 Mar '16

Hi All, Forwarding from GOBLET. Dave C ---------- Forwarded message ---------- From: Eija Korpelainen <eija.korpelainen(a)csc.fi> Date: Thu, Mar 24, 2016 at 7:31 AM Subject: Workshop "Using clouds and VMs in bioinformatics training", 23.-25.5 Finland To: Training-coordinators(a)elixir-europe.org, training(a)elixir-europe.org Cc: Timothy Stitt <timothy.stitt(a)tgac.ac.uk>, all(a)mygoblet.org Dear all, Please note that registration is now open for the Train-the-trainer workshop "Using clouds and VMs in bioinformatics training", which takes place at CSC in Finland 23.-25.5. This workshop introduces several cloud platforms from different countries, and bioinformatics trainers will gain hands-on experience in running VM images and Docker containers in them. The dialogue with bioinformatics trainers also allows infrastructure providers to gain valuable knowledge on the special needs that bioinformatics training poses. For more information about the program and practicalities, please see https://www.csc.fi/web/training/-/cloud-vm-bioinformatics The workshop is open for any bioinformatics trainer, so please feel free to distribute the information in your country. Places are filled in registration order and the registration can close earlier than 1.5.2016 if the workshop gets full. Should you have any questions regarding the workshop, please don't hesitate to contact me. Wishing you a chocolateful Easter, Eija Eija Korpelainen, Ph.D Product Manager, ELIXIR-FI training coordinator Application services, Bioinformatics CSC - IT Centre for Science P.O.Box 405 02101 Espoo, Finland Phone +358 50 381 9726 -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Fwd: Invitation from ISCB education committee related to tutorial topics
by Dave Clements 03 Mar '16

03 Mar '16

Hi All, The latest email from GOBLET. ISCB is looking to compile a list of "bioinformatics and computational biology tutorials at the meetings of other professional societies." See below if you have anything to add. Cheers, Dave C ---------- Forwarded message ---------- From: <Celia.vanGelder(a)radboudumc.nl> Date: Wed, Mar 2, 2016 at 10:42 PM Subject: Invitation from ISCB education committee related to tutorial topics To: all(a)mygoblet.org Dear all As member of the ISCB Education Committee I received the invitation below. Please spread this to people in your organization who would want to send a proposal. In addition, with our GOBLET hat on, I am sure we want to send in some of the topics we are working on together right now, and we can then brand them as GOBLET. Since this list is intended as tutorials for the meetings of other professional societies (e.g. life science, biology conferences ) I think it could be a very good route to bring our materials to the those communit ies. It is a channel that could be very useful for GOBLET. Best Celia *Van:* education(a)iscb.org [mailto:education@iscb.org <education(a)iscb.org>] *Namens *Welch, Lonnie *Verzonden:* woensdag 2 maart 2016 23:20 *Aan:* education(a)iscb.org *Onderwerp:* seeking tutorial proposals Dear ISCB Education Committee Members: The International Society for Computational Biology is working to facilitate the offering of bioinformatics and computational biology tutorials at the meetings of other professional societies. We are putting together a list of tutorial topics to share with the other societies. I invite you to send brief descriptions of tutorials that you’d be willing to offer in the general area of bioinformatics and computational biology education and training across the life sciences, including bioinformatics education and training resources and experiences; development of education programs, courses, & curricula; and teaching tools & methods. Best regards, Lonnie Welch Vice Chair of the ISCB Education Committee Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Re: [gxy-train] GOBLET/Elixir thematic hackaton for metagenomics training materials re-use | 6-8 April 2016
by Dave Clements 02 Mar '16

02 Mar '16

Dear Sarah and Gabry, I would like to confirm that the Galaxy Training Network is interested in participating in, and would like to send one or more people to this hackathon in April. We don't know who yet, but metagenomics is a key concern for the Galaxy community. (And we are holding a Metagenomics tools and workflows hack next week.) Do you need anything else from us at this time? Thanks, Dave C On Mon, Nov 23, 2015 at 2:58 AM, Gabriella Rustici <gr231(a)cam.ac.uk> wrote: > Dear all, > > You are invited to participate to the ‘GOBLET/Elixir thematic hackaton for > metagenomics training materials re-use’ that will take place in Copenhagen, > on 6-8 April 2016. > > The aim of this workshop is to bring together trainers and researchers > working in the field of metagenomics from within Europe and beyond, to > enhance the training network within this field. > > The workshop will focus on the curation of training materials in the area > of metagenomics data analysis, encompassing appropriate high-throughput > sequencing workflows (genome assembly, annotation and analysis) and related > subjects, such as phylogenetics and comparative genomics. > > Participants are expected to bring to the workshop the training materials > that they have developed in the domain of metagenomics data analysis. > > During the workshop we aim to: > > - Develop a collection of metagenomics training materials that are > consistently described, to enable sharing and re-use of such materials > across the training community; > - Define an approach for the curation of training materials for re-use > through training portals and repositories such as TeSS and the GOBLET > portal; and > - Link training materials to databases and standards in the BioSharing > registry and tools in the ELIXIR Tools & Data Services Registry. > > Funding is available for attendees that are not Elixir funded. > > Save the date and drop us an email to confirm your participation. > Additional information will follow shortly. > > Looking forward to see you in Copenhagen! > > Best regards, > > Sarah & Gabry > > -- > Gabriella Rustici, PhD > Bioinformatics Training Manager > > Department of Genetics > University of Cambridge > Downing Street > Cambridge CB2 3EH > United Kingdom > > Email: gr231(a)cam.ac.uk > Tel: +44 (0)1223 333614 > URL: http://training.csx.cam.ac.uk/bioinformatics/Event-timetable > > > -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Software Carpentry Webinar: Tuesday, March 8
by Dave Clements 02 Mar '16

02 Mar '16

Hello all, There is an upcoming webinar on Software Carpentry hosted by DataOne that might be interesting to this group: Research Computing Skills for Scientists: Lessons, Challenges, and Opportunities from Software Carpentry Tuesday March 8th 9 am Pacific / 10 am Mountain / 11am Central / 12 noon Eastern (those are all US times) See https://www.dataone.org/upcoming-webinar for more and the signup link. Thanks, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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GOBLET membership renewal (for GTN)
by Monica Britton 11 Feb '16

11 Feb '16

Hi Folks, Last week I received a reminder from GOBLET that my membership was due for renewal at the beginning of March, and I'm wondering if the same five groups will be renewing this year? Although I read the emails related to GTN/GOBLET, I admit I have not been an active participant, and have not even figured out how to switch the membership from being under my personal name to "UC Davis Bioinformatics Training Program". (Is that possible?) There was some discussion post-GOBLET meeting for building the GTN-GOBLET relationship. Has any of that been decided? Thanks in advance for your advice. Monica Britton Sr. Bioinformatics Analyst Genome Center and Bioinformatics Core Facility University of California, Davis mtbritton(a)ucdavis.edu

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Fwd: ECCB 2016 - Call for proposals for Workshops & Tutorials - deadline January 13
by Dave Clements 04 Jan '16

04 Jan '16

Hello all, Forwarding from the GOBLET mailing list. Dave C ---------- Forwarded message ---------- From: <Celia.vanGelder(a)radboudumc.nl> Date: Mon, Jan 4, 2016 at 1:39 AM Subject: ECCB 2016 - Call for proposals for Workshops & Tutorials - deadline January 13 To: all(a)mygoblet.org Dear colleague, Let me start by wishing you all a very happy and healthy 2016!! As you may already know the ECCB 2016 <http://www.eccb2016.org/> will be organised from September 3-7 2016 in The Hague, The Netherlands. The workshops and tutorials will be held on September 3 or 4. I am Tutorial Chair. You are very welcome to submit a proposal for a workshop or tutorial! *The submission deadline for proposals is January 13, 2016.* Please let me know if you need more information . All guidelines can be found here: http://www.eccb2016.org/calls/ Best, Celia Dr. Celia W.G. van Gelder Education Manager BioSB Coordinator Education CMBI Programme Manager Learning DTL/ELIXIR-NL tel. +31613375327 e-mail: Celia.vanGelder(a)radboudumc.nl websites: www.nbic.nl, www.biosb.nl, www.cmbi.ru.nl, www.dtls.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre PO Box 9101 6500 HB Nijmegen The Netherlands Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Fwd: [Discuss] Data Carpentry is hiring an Associate Director
by Dave Clements 10 Dec '15

10 Dec '15

Hi All, There's an opening at Data Carpentry for an Associate Director "who is passionate about education and training and its ability to empower researchers to conduct data-driven research." (That could easily describe the Galaxy training community. :-) If you know anyone who might be interested, then please pass this along. Application review starts Dec 18. Cheers, Dave C ---------- Forwarded message ---------- From: Tracy Teal <tkteal(a)gmail.com> Date: Mon, Nov 30, 2015 at 3:51 PM Subject: [Discuss] Data Carpentry is hiring an Associate Director To: discuss(a)lists.software-carpentry.org Data Carpentry is hiring! http://www.datacarpentry.org/blog/associate-director-posting/ With the support of the Gordon and Betty Moore Foundation, we now have the opportunity to hire an Associate Director. The Associate Director is one of the two key roles providing leadership to Data Carpentry’s core efforts and is expected to shape the organization’s operational functioning, influence training, and contribute to strategic planning. The main focus of the Associate Director’s role will be in working with Software Carpentry on community engagement and education as well as overseeing Data Carpentry communications. Mainly though, we’re looking for someone who is passionate about education and training and its ability to empower researchers to conduct data-driven research. This person should also have a background in education or research and experience with volunteer communities and demonstrated leadership. This obviously includes many people on this list, and we would love, love, love applications from Software and Data Carpentry instructors. If you have any questions about the position, please don't hesitate to contact me at tkteal(a)datacarpentry.org Best, -Tracy _______________________________________________ Discuss mailing list Discuss(a)lists.software-carpentry.org http://lists.software-carpentry.org/mailman/listinfo/discuss_lists.software… -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Galaxy Training Network items for 2015 GOBLET Meeting
by Dave Clements 18 Nov '15

18 Nov '15

Hello Fourie, Terri, Michelle, and Peter, (and the Galaxy training community) The Galaxy training community has discussed what we would like to see in GOBLET in the coming year. I initially floated several ideas on the galaxy-training mailing list, and these were then modified and extended by the community. This email lists those items and includes some suggestions for implementing them. Fourie, we're handing these to you for presenting to the larger group. Peter van Heusden of SANBI will also be in attendance and can also speak from his experience within the Galaxy community. Many thanks for Hans-Rudolf Hotz and Björn Grüning for starting this conversation and contributing to it, and to Fourie for agreeing to represent GTN. If anyone has anything to add to the items below, please do so in the next day. Thanks, and have a great meeting, Dave C on behalf of the Galaxy Training Network *Five items we would like to see discussed are:* *1. Enable/Host online discussion about bioinformatics training.* We'd like GOBLET to host a mailing list or online forum for discussion of bioinformatics training issues. GOBLET has an announcements mailing list, but it would be a huge win if GOBLET hosted *the* place to discuss bioinformatics training issues. We argue this place list/forum be open to anyone, not just GOBLET members. Galaxy has had significant success with a Biostar based forum (but a mailing list would be great too.) *2. Either start sending a regular newsletter, or stop saying we have one.* Our preference is to start sending a regular newsletter, but that is effort and the payoff is uncertain. Having a newsletter does increase GOBLET's visibility and it also great for newcomers to see what is going on. (And having a better welcome for new GOBLETeers is one of our goals.) I prepare the monthly Galaxy Newsletters and this takes a little over a day of my time, every month. (But when I suggested to the Galaxy training list, that this might not be worth my time, I got pushback that it was worth my time.) *3. Should GOBLET offer a bioinformatics trainer certification?* GTN is in favor of a GOBLET Trainer badge as a way of both promoting GOBLET and as a way of saying "I've participated in GOBLET training" or "I'm GOBLET certified." Perhaps attendees at the just finished best practices workshop would be the first recipients? *4. Make it easier to publish, share, and refine training material.* (I'm channeling Björn Grüning here. Björn, please correct me if I go astray.) Software and Data Carpentry's model for training material is to use GitHub for version control, and to use Github's branching and merging capabilities to enable community editing of that training material. Right now GOBLET's (and GTN's) training material sharing is purely upload/download. It might be worth considering taking a hard look at how Carpentry does this and then support a similar model. Embracing this might lead to an explosion of collaboration on training material. It has been very successful for Software Carpentry The danger here is that the upload/download model is simple to use and easy to implement, and a Github based system would be a lot of work up front, and might not ever catch on. *5. Shared Training Datasets are Precious!* (Also channeling Björn here, although he never used the word "precious.") Given the difficulty and time required to create good datasets for training, it might be worthwhile for GOBLET to create a central repository for training datasets. This increases their visibility and usefulness, and also increases the visibility of the training dataset creators. Right now people can upload datasets of up to 50MB, which is good, but it would be great if there were some way to identify just training datasets, or training resources that include datasets. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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GCC2016 Topic Nomination: Galactically Speaking: Best Practices and Resources for Galaxy Training
by Dave Clements 10 Nov '15

10 Nov '15

Hi All, In the wake of the Carpentry TTT workshop not being scheduled for GCC2016, Mo Heydarian (CC'd here) suggested that perhaps we have a much lighter-weight session during GCC2016 training that covers best practices and resources for training with Galaxy. Mo and I scrambled our brains together and came up with this nomination: http://bit.ly/1LTdwtV We would love to have feedback on this proposal, both specific and big picture. The text of the nomination can easily be updated any time between now and next Monday, when voting opens. This is an opportunity to gather best practices into a single place, and would be a friendly place to bring new trainers into the fold. Also, please let me know if you'd be interested in helping teach this. Thanks, and many thanks to Mo for making this happen, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Call for HELP with teaching GCC2016 Training Topics!
by Dave Clements 24 Oct '15

24 Oct '15

Hello all, Most GCC2016 training nominations have now been posted to https://wiki.galaxyproject.org/Events/GCC2016/Training And we ... *Need possible Instructors for ...* Most of those nominations included the nominator as a suggested instructor, but some did not. Voting doesn't open for another week, but I'd like to start work on identifying instructors for the course we don't have names for: - Small Genomes de novo Assembly and Scaffolding <https://wiki.galaxyproject.org/Events/GCC2016/Training#Small_Genomes_de_nov…> - Small Genome Annotation <https://wiki.galaxyproject.org/Events/GCC2016/Training#Small_Genome_Annotat…> - RNA-seq analysis with Galaxy, using advanced workflows <https://wiki.galaxyproject.org/Events/GCC2016/Training#RNA-seq_analysis_wit…> - Phylogeny, Species identification (16S and 18S metagenomics tools) and Viral detection tools <https://wiki.galaxyproject.org/Events/GCC2016/Training#Phylogeny.2C_Species…> - Antibiotics resistance predictions, Virulence genes, Insertion sequences, Phages and Plasmid profiling <https://wiki.galaxyproject.org/Events/GCC2016/Training#Antibiotics_resistan…> If you have any interest in teaching, or have ideas on who could teach these topics, please let me know. Potential instructors can update the text of any workshop topic that they take on. *Need a topic description for ...* Finally, we have one topic that we only have a very short description for this workshop nomination: - ChIP-Seq data analyses <https://wiki.galaxyproject.org/Events/GCC2016/Training#ChIP-Seq_data_analys…> This topic was nominated by Nobuo Horikoshi (cc'd here). Nobuo's particular concerns are ... guidelines strongly recommend biological replicates for ChIP-Seq but > handling replicates are not well described/developped in Galaxy yet. > Furthermore, the most common IDR calculation for MACS is not suitable for > SICER peak calling. Therefore, I thought handling biological replicates is > practically essential task in Galaxy. I've asked some folks with a deeper understanding of ChIP-Seq if they could transform Nobuo's description into a workshop description, but so far, no one has embraced that task. If anyone on this list feels up that task, please let Nobuo and myself know. It would be nice to have a fuller description up no later than next Monday. Thanks everyone, Dave C. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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