Galaxy-training

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87 discussions

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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GCC2016 and a Software/Data Carpentry Train the Trainer Session
by Dave Clements 12 Oct '15

12 Oct '15

Hello all, We are considering offering a Software Carpentry <https://software-carpentry.org/> / Data Carpentry <http://www.datacarpentry.org/> *Train the Trainer* workshop immediately before GCC2016 <http://galaxyproject.org/GCC2016>. This workshop would run for two days, and accommodate 24 people. *Why?* This idea came up at the GCC2015 GTN BoF <http://bit.ly/gcc2015gtnbof>. Software and Data Carpentry (S/DC) teach scientists core essentials of programming and data management. Their model is to train and certify trainers, and then provide a common curriculum and teaching infrastructure that enables those trainers to teach scientists how to program and manage data well. We think a S/DC Train the Trainer workshop would be a huge benefit to the Galaxy Training community for many reasons: - *The researchers we teach bioinformatics and Galaxy to would also benefit from learning S/DC*. Becoming certified S/DC instructors would give us additional (and extremely useful) topics that we could also teach to our communities. - *The techniques presented in S/DC Train the Trainer workshops are equally applicable to bioinformatics and Galaxy training*. Attending a S/DC TTT workshop would improve the training we already do. - *The organizational and compute infrastructure supporting S/DC might make an excellent model for the Galaxy Training Network*. S/DC has embraced technologies like GitHub for storing, sharing, and maintaining training materials and best practices. We can learn from their significant experience to make GTN a much more vibrant community. *But, Should We?* However, before we put in the organizational effort (and funds) to make a Train the Trainer workshop happen at GCC2016, we'd like to know what the Galaxy Training community thinks of this proposal. In particular: *1. Are S/DC techniques and training methods a good match for Galaxy trainers?* We'd especially like to hear from you if are a certified SC or DC instructor. *2. Is the S/DC content a good match for the researchers that we train?* We'd especially like to hear from anyone who has attended an S/DC workshop. *3. Might the S/DC organizational and infrastructure make a good model for GTN?* *4. Would you likely attend a Train the Trainer workshop before GCC2016?* The workshop would be in Bloomington, Indiana, most likely offered on Thursday-Friday, June 23-24. Registration would likely be between US$200 and $300. (And no, that would not cover the costs - the workshop would be subsidized by some combination of the project and the meeting.) If and when we decide that this is a good idea, I'll start getting everything arranged to make this happen. Ideally, we would have a decision within a week or two. Thanks, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Do Training? Add yourself to the myGOBLET.org trainer directory
by Dave Clements 11 Oct '15

11 Oct '15

Hello all, This thread about GTN at the 2015 GOBLET meeting <http://bit.ly/1iM6T5r> mentioned this item: *1. Increase the visibility of all GTN members within GOBLET* GTN now has 26 members (please welcome Noor Biotechnologies, by the way - > tweet going out on Monday*). Can we get all GTN members (not just the > member that paid) listed in the trainer directory? > It turns out that we can do that now. If you want to be listed as a trainer on the GOBLET website, register as a contributor here: http://www.mygoblet.org/user/register This creates an account and allows you to create links to your training material. If you are a member of GTN, then please also send your username to me. I'll add your account to the GTN umbrella ( http://mygoblet.org/about-us/affiliations/GTN) Thanks, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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GTN issues for GOBLET Meeting in October?
by Dave Clements 08 Oct '15

08 Oct '15

Hello all, After watching from afar, I decided to attend last year's GOBLET meeting in Toronto. I was impressed enough with that meeting to argue that GTN should become a member of GOBLET in 2015, and thanks to the contributions of 5 GTN member organizations, GTN is now a member of GOBLET. The 2015 GOBLET meeting will be in Cape Town in November. GTN will be represented by Fourie Joubert of the University of Pretoria. Fourie is our first GTN member in Africa and has been teaching bioinformatics with Galaxy for several years. I'd like to start a discussion about the issues that GTN cares about and how we can help GOBLET, and how GOBLET can help us. Fourie can then raise whatever issues we identify at the meeting. If you have items for discussion, please post them to this thread. I'll post something in the next day or two. And many thanks to Hans-Rudolf Hotz and Björn Grüning for raising the GTN/GOBLET 2015 question with me, and to Fourie for agreeing to represent GTN at this meeting. Cheers, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Fwd: GCC2016 Training Day Topic Nominations are now open
by Dave Clements 05 Oct '15

05 Oct '15

Hello all, The call for GCC2016 training topic nominations just went out. Many of you would make great GCC2016 training topic presenters so please give this some thought. Nominations close on October 16. Something new this year is that we will have two full days of multi-track training. This gives us much more flexibility than in previous years. In particular we are open to proposals that span more than one session. We've always been open to complementary/coordinated multi-topic nominations. For example, The Tool related topics have been coordinated every year (I think). Please post any questions to me or the list (if it's a question everyone would benefit from, then the list is preferred). Thanks for everything, Dave C ---------- Forwarded message ---------- From: Dave Clements <clements(a)galaxyproject.org> Date: Mon, Sep 28, 2015 at 11:34 AM Subject: GCC2016 Training Day Topic Nominations are now open To: Galaxy Announcements List <galaxy-announce(a)lists.galaxyproject.org>, Galaxy Dev List <galaxy-dev(a)lists.galaxyproject.org> Hello all, The 2016 Galaxy Community Conference (GCC2016) <https://wiki.galaxyproject.org/Events/GCC2016> features two full days of training on June 26-27. Each day will have multiple tracks, with each track featuring several sessions throughout the day. GCC2016 will be held at Indiana University <http://indiana.edu/> in Bloomington, Indiana, United States. *GCC2016 Training topics <https://wiki.galaxyproject.org/Events/GCC2016/Training> are nominated by you <http://bit.ly/gcc2016tdnom>, the Galaxy Community.* Please give some thought to what topics you would like to see offered, or that you would like to offer, and then submit them as topic nominations <http://bit.ly/gcc2016tdnom>. Any topic of interest to the Galaxy Community can be nominated and you are encouraged to nominate more than one topic. If you are looking for ideas, see - Topics nominated for GCC2015 <http://bit.ly/gcc2015vote> - Topics nominated for GCC2014 <http://bit.ly/1s6NtMN> - Topics nominated for GCC2013 <http://bit.ly/1i2j1gN> - The Galaxy Events page <https://wiki.galaxyproject.org/Events>, which lists what training the community is offering outside of GCCs. - Topics that have already been nominated for GCC2016 <https://wiki.galaxyproject.org/Events/GCC2016/Training#Nominated_Topics> *Please nominate a topic now! <http://bit.ly/gcc2016tdnom> * Nominated topics will be published as they come in <https://wiki.galaxyproject.org/Events/GCC2016/Training#Nominated_Topics>. *Topic nomination closes Friday, October, 16.*. Topics will be compiled into a uniform list by the GCC2016 Organizing Committee, and topics will be voted on by the Galaxy Community from October 26 through November 6. Topics will then be selected and scheduled based on topic interest, and the organisers' ability to confirm instructors for each session. Some very popular sessions may be scheduled more than once. The final schedule will be posted before registration opens. Looking forward to a stellar set of nominations, and hoping to see you in Bloomington, GCC2016 Exec Committee <https://wiki.galaxyproject.org/Events/GCC2016/Organizers> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Fwd: Metagenomics training materials hackaton - April 2016
by Dave Clements 10 Sep '15

10 Sep '15

Hello all, If you do metagenomics training, then this may be of interest to you. Cheers, Dave C ---------- Forwarded message ---------- From: Gabriella Rustici <gr231(a)cam.ac.uk> Date: Thu, Sep 10, 2015 at 2:51 AM Subject: Metagenomics training materials hackaton - April 2016 To: "all(a)mygoblet.org" <all(a)mygoblet.org> Dear GOBLET members, GOBLET and Elixir are planning a joint hackathon for metagenomic training material re-use, to take place in Copenhagen in 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, encompassing appropriate high-throughput sequencing workflows (genome assembly, annotation and analysis) and related subjects, such as phylogenetics and comparative genomics. During the workshop we aim: - to develop a collection of metagenomics training materials that are consistently described, to enable sharing and re-use of these materials across the training community; - to define an approach for the curation of training materials for re-use through training portals and repositories such as TeSS and GOBLET; and - to link training materials to tools in the "ELIXIR Tools & Data Services Registry". In order to achieve this, we would like to invite metagenomics trainers from GOBLET to participate to this workshop, bring their own training materials and work collaboratively to annotate them in a consistent manner. We expect around 30 participants, representing both Elixir and GOBLET, to attend this event. If you have developed training materials in the analysis of metagenomics data and are interested in attending such workshop, please email Gabriella Rustici (gr231(a)cam.ac.uk) or Sarah Morgan (sarah.morgan(a)ebi.ac.uk) by *Friday 25th September *to state your interest. We would be grateful if you could also send us a brief description of your training involvement so far. We look forward to hear from you. Best regards, Gabry & Sarah -- 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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Fwd: [Bioinformatics] Bioinformatics Trainer Workshop
by Dave Clements 04 Sep '15

04 Sep '15

Hello all, The latest addition to the GOBLET meeting in Cape Town. Please do respond to this thread (or one of Björn's) if you are planning to attend any part of the GOBLET meeting. Thanks, Dave C ---------- Forwarded message ---------- From: Nicola Mulder <nicola.mulder(a)uct.ac.za> Date: Mon, Aug 31, 2015 at 1:26 PM Subject: [Bioinformatics] Bioinformatics Trainer Workshop To: "bioinformatics(a)bioinformatics.org.za" < bioinformatics(a)bioinformatics.org.za>, "bioinf-directors(a)lists.wits.ac.za" < bioinf-directors(a)lists.wits.ac.za>, "abec(a)lists.h3abionet.org" < abec(a)lists.h3abionet.org>, Vernon Coyne <vernon.coyne(a)uct.ac.za>, Nicola Illing <nicola.illing(a)uct.ac.za>, "idm-staff-l(a)lists.uct.ac.za" < idm-staff-l(a)lists.uct.ac.za> Cc: Anthony Beitz <anthony.beitz(a)uct.ac.za>, "anelda(a)talarify.co.za" < anelda(a)talarify.co.za>, "announce(a)lists.h3abionet.org" < announce(a)lists.h3abionet.org> Dear Current and Potential Bioinformatics Trainers We will be running a Best practices in Bioinformatics Training workshop organised by the Global Organisation for Bioinformatics Learning, Education and Training (GOBLET) and H3ABioNet in Cape Town from the 16-17th November. The first day will cover aspects of teaching and the second day will be more of an interactive workshop to discuss bioinformatics curricula, course materials, trainer recognition, etc. This “train-the-trainer” course is designed for anyone who currently teaches or plans to teach bioinformatics both in universities as part of degree programs or as short specialised courses. Attached please find some more details on the workshop, including the agenda, venue and how to apply. The deadline is *25th September 2015*. Please forward to anyone who you think may be interested. Regards Nicky Professor Nicola Mulder Head of Computational Biology Group H3ABioNet Principal Investigator University of Cape Town ------------------------------ UNIVERSITY OF CAPE TOWN This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111. This e-mail is intended only for the person(s) to whom it is addressed. If the e-mail has reached you in error, please notify the author. If you are not the intended recipient of the e-mail you may not use, disclose, copy, redirect or print the content. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity. _______________________________________________ Bioinformatics mailing list Bioinformatics(a)bioinformatics.org.za http://www.bioinformatics.org.za/mailman/listinfo/bioinformatics -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Fwd: An ELIXIR/GOBLET workshop: defining an e-learning lingua franca
by Björn Grüning 24 Aug '15

24 Aug '15

Hi Trainers! Anyone interested in joining? Cheers, Bjoern ------------- Dear GOBLET members, ELIXIR and GOBLET are organising a workshop to discuss e-learning strategies. It will take place at the Faculty of Medicine, University of Ljubljana, Slovenia on 15-17 September 2015. This workshop will provide an overview of e-learning systems used within ELIXIR and GOBLET. The aim is to compare them, to understand their respective strengths and weaknesses, and to define a common e-learning ‘language’ to facilitate communication within and between the GOBLET and ELIXIR trainer communities. The outcomes of the workshop will be summarised in a draft white paper, describing the various e-learning approaches and their applications, and providing recommendations for their use. You will find more information about this workshop and the registration at: http://www.mygoblet.org/about-us/goblet-events/elixirgoblet-workshop-defini… All the best, Patricia -- Patricia M. Palagi, Ph.D. Head, Training and Outreach SIB|Swiss Institute of Bioinformatics CMU Unil, CIG 1 Michel-Servet Quartier Sorge, Genopode CH-1211 Geneva 4 CH-1015 Lausanne Switzerland Mon, Wed (+41 22) 379 5831 Tue, Thu (+41 21) 692 4078 Patricia.Palagi(a)isb-sib.ch http://www.isb-sib.ch/training _________________________________________________________________________

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