2024-03-28T21:15:45Z
https://zenodo.org/oai2d
oai:zenodo.org:4030401
2022-05-17T10:53:08Z
user-goblet
openaire
Psomopoulos, Fotis
2020-09-15
<p>A short presentation done in the context of the GOBLET AGM 2020, offering an overview of the online training for Machine Learning that took place using the Galaxy infrastructure.</p>
https://doi.org/10.5281/zenodo.4030401
oai:zenodo.org:4030401
eng
Zenodo
https://zenodo.org/communities/goblet
https://doi.org/10.5281/zenodo.4030400
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
bioinformatics
online training
galaxy
machine learning
Delivering hands-on training for Machine Learning on omics data through GALAXY
info:eu-repo/semantics/lecture
oai:zenodo.org:4053050
2023-07-20T14:09:12Z
user-goblet
openaire
user-sib-training
user-elixir
Garcia, Leyla
Palagi, Patricia M.
on behalf of the ELIXIR FAIR Training group
2020-09-27
<p>Sharing, reusing and reproducing data, software and other digital objects are the basis for open science practices, and to ease this the scientific community has developed the Findable, Accessible, Interoperable and Reusable (FAIR) principles. </p>
<p>The <a href="https://elixir-europe.org/platforms/training">ELIXIR Training Platform</a> has put together a <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007854">Ten Simple Rules for Making Training Materials FAIR</a> paper which apply the FAIR principles to training materials, a type of digital object. In this paper, the FAIR principles are broken down into very practical steps. This webinar introduced these ten rules and discussed the challenges and ideas to put them into practice. </p>
https://doi.org/10.5281/zenodo.4053050
oai:zenodo.org:4053050
eng
Zenodo
https://doi.org/10.1371/journal.pcbi.1007854
https://zenodo.org/communities/sib-training
https://zenodo.org/communities/goblet
https://zenodo.org/communities/elixir
https://doi.org/10.5281/zenodo.4053049
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
FAIR principles
Training Materials
Trainers
Trainees
Training
Ten simple rules to make training materials FAIR - ELIXIR webinar on 17 Sep 2020
info:eu-repo/semantics/lecture
oai:zenodo.org:4783481
2021-06-02T16:28:22Z
user-goblet
Meeta Mistry
Mary Piper
Jihe Liu
Radhika Khetani
2021-05-24
<p>First release of the differential gene expression analysis for bulk RNA-seq data training materials from the Harvard Chan Bioinformatics Core (<a href="https://bioinformatics.sph.harvard.edu/training">https://bioinformatics.sph.harvard.edu/training</a>). The count data are obtained by running Salmon on the bulk RNA-seq dataset from Kenny PJ et al. Cell Reports 2014 (DOI: <a href="https://doi.org/10.1016/j.celrep.2014.10.054">10.1016/j.celrep.2014.10.054</a>).</p>
<p>These training materials utilize many R packages with a focus on the following packages:</p>
<ul>
<li>DESeq2</li>
<li>clusterProfiler</li>
<li>AnnotationHub</li>
</ul>
https://doi.org/10.5281/zenodo.4783481
oai:zenodo.org:4783481
Zenodo
https://github.com/hbctraining/DGE_workshop_salmon_online/tree/1.0.0
https://zenodo.org/communities/goblet
https://doi.org/10.5281/zenodo.4783480
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
R
DESeq2
differential gene expression
functional analysis
clusterprofiler
bulk RNA-seq
hbctraining/DGE_workshop_salmon_online: Differential Gene Expression Workshop Lessons from HCBC (first release)
info:eu-repo/semantics/lecture
oai:zenodo.org:4739342
2021-06-02T16:28:25Z
user-goblet
Meeta Mistry
Mary Piper
Jihe Liu
Radhika Khetani
2021-05-05
<p>First release of R training materials from the Harvard Chan Bioinformatics Core (<a href="https://bioinformatics.sph.harvard.edu/training">https://bioinformatics.sph.harvard.edu/training</a>). </p>
<p>These training materials aim to address the following learning objectives:</p>
<p>* Understand the different 'parts of speech' in R.<br>
* Describe the various data types and data structures.<br>
* Demonstrate the utilization of functions and indices to inspect and subset data from various data structures.<br>
* Demonstrate the use of the ggplot2 package to create plots for easy data visualization.</p>
https://doi.org/10.5281/zenodo.4739342
oai:zenodo.org:4739342
eng
Zenodo
https://github.com/hbctraining/Intro-to-R-flipped/tree/1.0.1
https://zenodo.org/communities/goblet
https://doi.org/10.5281/zenodo.4739341
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
R
bioinformatics education
hbctraining/Intro-to-R-flipped: R workshop first release
info:eu-repo/semantics/lecture
oai:zenodo.org:5825871
2023-03-11T17:59:50Z
user-goblet
Meeta Mistry
Shannan Ho Sui
Jihe Liu
Mary Piper
William Gammerdinger
Radhika Khetani
2022-01-06
<p>First release of the ChIP-seq data analysis training materials from the Harvard Chan Bioinformatics Core (<a href="https://bioinformatics.sph.harvard.edu/training">https://bioinformatics.sph.harvard.edu/training</a>). The raw data was obtained from the SRA (<a href="https://www.ncbi.nlm.nih.gov/sra?term=SRP134733">https://www.ncbi.nlm.nih.gov/sra?term=SRP134733</a>).</p>
<p>Learning Objectives</p>
<ul>
<li>Understand the necessity for, and use of, the command line interface (bash) and HPC for analyzing high-throughput sequencing data.</li>
<li>Understand best practices for designing a ChIP-seq experiment and analysis the resulting data.</li>
</ul>
<p>Description This workshop focuses on teaching computational skills to enable the effective use of an high-performance computing environment to implement a ChIP-seq data analysis workflow. In addition to running the workflow from FASTQ files to peak calls, the workshop covers best practice guidelines for ChIP-seq experimental design and data organization/management and data visualization for quality control.</p>
<ul>
<li>Introduction to ChIP-seq</li>
<li>QC using FASTQC</li>
<li>Alignment and filtering of reads (Bowtie2, Samtools)</li>
<li>Peak calling (MACS2)</li>
<li>Peak overlap (bedtools)</li>
<li>Peak visualization (using deepTools)</li>
</ul>
https://doi.org/10.5281/zenodo.5825871
oai:zenodo.org:5825871
Zenodo
https://github.com/hbctraining/Intro-to-ChIPseq-flipped/tree/chip-seq
https://zenodo.org/communities/goblet
https://doi.org/10.5281/zenodo.5825870
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
chip-seq, macs2
hbctraining/Intro-to-ChIPseq-flipped: ChIP-seq Data Analysis Lessons from HCBC (first release)
info:eu-repo/semantics/lecture
oai:zenodo.org:8048971
2023-06-19T06:09:32Z
user-goblet
openaire
user-sib-training
Palagi, Patricia M.
2023-06-13
<p>A hands-on self-learning handbook on how to FAIRify training materials was designed, created, implemented and improved on several occasions within ELIXIR and international events: in 2021 during ELIXIR hackathons, at the GOBLET AGM 2022, and recently at the Biohackathon Europe 2022. The first version of the <a href="https://elixir-europe-training.github.io/ELIXIR-TrP-FAIR-training-handbook/"> FAIR Training Material handbook</a> was released in March 2023, and that thanks to the contribution from several international collaborators. At the Work-on FAIR training materials, ELIXIR session, during the X-Meeting, Brazil, we have illustrated all the steps to FAIRify training materials with the SIB Swiss Institute of Bioinformatics use case.</p>
https://doi.org/10.5281/zenodo.8048971
oai:zenodo.org:8048971
eng
Zenodo
https://zenodo.org/communities/sib-training
https://zenodo.org/communities/goblet
https://doi.org/10.5281/zenodo.8048970
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
X-Meeting, Curitiba, Brazil, Curitiba, Brazil, 13-16 June 2023
FAIR
training
training material
open
metadata
repositories
license
Checking the FAIRification of training materials at SIB Swiss Institute of Bioinformatics
info:eu-repo/semantics/lecture
oai:zenodo.org:5937856
2022-05-17T10:53:06Z
user-goblet
openaire
user-dtl
Bernardi, Maria Trinidad
Carvajal-López, Patricia
van Gelder, Celia WG
Merino, Gabriela Alejandra
Morgan, Sarah L
Mulder, Nicola
De Las Rivas, Javier
Yam, Wai Keat
2022-02-01
<p>The Bioinformatics Education Summit is an online working meeting to develop guides, papers and documents for promoting and improving <strong>Education and Training in Bioinformatics</strong> worldwide.The participation is free and open to all people working in the area of Bioinformatics teaching and education or who have a clear interest in contributing to it.</p>
<p>2021’s iteration of this virtual event was organized by<a href="http://www.google.com/url?q=http%3A%2F%2Fwww.cabana.online&sa=D&sntz=1&usg=AFQjCNGbsG3U3IXS2xc6XHRwGq9Kl6Ungg"> </a><a href="http://www.google.com/url?q=http%3A%2F%2Fwww.cabana.online&sa=D&sntz=1&usg=AFQjCNGbsG3U3IXS2xc6XHRwGq9Kl6Ungg">CABANA</a>,<a href="https://www.google.com/url?q=https%3A%2F%2Fwww.mygoblet.org%2F&sa=D&sntz=1&usg=AFQjCNF1pDA-tI3P2jVLaOYg0Z-hfdzElA"> </a><a href="https://www.google.com/url?q=https%3A%2F%2Fwww.mygoblet.org%2F&sa=D&sntz=1&usg=AFQjCNF1pDA-tI3P2jVLaOYg0Z-hfdzElA">GOBLET</a>,<a href="https://www.google.com/url?q=https%3A%2F%2Felixir-europe.org%2F&sa=D&sntz=1&usg=AFQjCNFTH9PKQAzoWrLHqPCf4bx5pgxq4g"> </a><a href="https://www.google.com/url?q=https%3A%2F%2Felixir-europe.org%2F&sa=D&sntz=1&usg=AFQjCNFTH9PKQAzoWrLHqPCf4bx5pgxq4g">ELIXIR</a>,<a href="https://www.google.com/url?q=https%3A%2F%2Fwww.h3abionet.org%2F&sa=D&sntz=1&usg=AFQjCNEMyOf4vNHmSw7TGglqB2zEJ5ACqA"> </a><a href="https://www.google.com/url?q=https%3A%2F%2Fwww.h3abionet.org%2F&sa=D&sntz=1&usg=AFQjCNEMyOf4vNHmSw7TGglqB2zEJ5ACqA">H3ABioNet</a>,<a href="https://www.google.com/url?q=https%3A%2F%2Fwww.apbionet.org%2F&sa=D&sntz=1&usg=AFQjCNF-nsMTCIT2W7q9TSGQnNCdIpK-Uw"> </a><a href="https://www.google.com/url?q=https%3A%2F%2Fwww.apbionet.org%2F&sa=D&sntz=1&usg=AFQjCNF-nsMTCIT2W7q9TSGQnNCdIpK-Uw">APBioNET</a> and<a href="https://www.google.com/url?q=https%3A%2F%2Fwww.iscb.org%2F&sa=D&sntz=1&usg=AFQjCNHCOSBSLWzVoKV3piJWh3c5Ew3HdQ"> </a><a href="https://www.google.com/url?q=https%3A%2F%2Fwww.iscb.org%2F&sa=D&sntz=1&usg=AFQjCNHCOSBSLWzVoKV3piJWh3c5Ew3HdQ">ISCB</a>. It was held from the <strong>24th-26th</strong> <strong>May, 2021. </strong>This year in particular we were welcoming a wider body of academics, researchers, representatives and stakeholders from all over the world, thus, all working days were divided in three Time Zones.</p>
<p>This presentation is a summary of the Outcomes and Next Steps of the Education Summit 2021. It was presented by members of the Organising Committee at ISMB 2021 and at the GOBLET AGM2021.</p>
<p> </p>
https://doi.org/10.5281/zenodo.5937856
oai:zenodo.org:5937856
Zenodo
https://zenodo.org/communities/dtl
https://zenodo.org/communities/goblet
https://doi.org/10.5281/zenodo.5937855
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
bioinformatics
training
education
skills
competences
FAIR
LMIC
2021 Bioinformatics Education Summit - Summary & Outlook
info:eu-repo/semantics/lecture
oai:zenodo.org:5820221
2022-08-04T08:36:59Z
user-goblet
openaire
user-dtl
user-sib-training
user-galaxy-training
user-australianbiocommons
Hiltemann, Saskia
Swan, Anna
Ras, Verena
Doyle, Maria
Burke, Melissa
Palagi, Patricia M.
van Gelder, Celia W.G.
2021-07-25
<p>Sharing data has become common practice around the globe, and training is part of this trend. <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007854">This PLoS 10 simple rules paper </a>published in 2020 introduced tips and tricks on how to make training materials FAIR (Findable, Accessible, Interoperable and Reusable), which encouraged trainers to share their materials with others, and facilitated this process. </p>
<p>The WEB (Workshop on Education for Bioinformatics) 2021 was a dedicated forum for training providers, trainers and trainees to share their experiences of making training materials FAIR. The WEB was composed of short presentations from invited speakers who have been through this process, where they have introduced their approaches, challenges and solutions. </p>
https://doi.org/10.5281/zenodo.5820221
oai:zenodo.org:5820221
eng
Zenodo
https://zenodo.org/communities/sib-training
https://zenodo.org/communities/dtl
https://zenodo.org/communities/goblet
https://zenodo.org/communities/australianbiocommons
https://zenodo.org/communities/galaxy-training
https://doi.org/10.5281/zenodo.5820220
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
ISMB ECCB 2021, 29th Conference on Intelligent Systems for Molecular Biology and 20th European Conference on Computational Biology - 2021, 25-30 July 2021
FAIR, FAIR principles, training, training materials, implementation, challenges, solutions, experiences
Making training materials FAIR experiences, challenges, solutions
info:eu-repo/semantics/lecture
oai:zenodo.org:5646887
2022-05-17T10:58:04Z
user-goblet
openaire
user-dtl
Celia W.G. van Gelder
2021-11-05
<p>This is the Executive Board report 2021 that was presented on the GOBLET Annual General Meeting at October 12, 2021 by Celia van Gelder, Chair of GOBLET, on behalf of the GOBLET Executive Board.</p>
https://doi.org/10.5281/zenodo.5646887
oai:zenodo.org:5646887
Zenodo
https://zenodo.org/communities/dtl
https://zenodo.org/communities/goblet
https://doi.org/10.5281/zenodo.5646886
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
training
education
GOBLET
global community
bioinformatics
GOBLET Annual General Meeting 2021 - Executive Board Report
info:eu-repo/semantics/lecture
oai:zenodo.org:166378
2023-07-20T14:10:29Z
user-goblet
user-dtl
user-sib-training
user-elixir
user-eu
Attwood, Teresa K.
Leskosek, Brane L.
Dimec, Jure
Morgan, Sarah
Mulder, Nicola
van Gelder, Celia W.G.
Palagi, Patricia M.
2016-11-13
<p>Today, the term <strong>e-learning</strong> is widely used in a variety of contexts. Many of us are familiar with concepts like <strong>Massive Open Online Courses</strong> (MOOCs), such as those provided by Coursera, Udacity, edX or MIT OpenCourseWare; <strong>Content</strong>- or <strong>Learning-Management Systems</strong> (CMSs, LMSs), like Moodle or Blackboard; <strong>Virtual Learning Environments</strong> (VLEs), like EMBER; problem and tutorial portals, such as Rosalind and Train online; repositories for uploading and hosting <strong>Educational Resources</strong> (ERs), such as that provided by GOBLET; <strong>ER aggregators</strong> that harvest and disseminate training information, such as TeSS; and so on. Resources like these are seamlessly discussed under the umbrella term ‘e-learning’; however, they are heterogeneous and do not mean the same thing from user, developer, trainer or content-provider perspectives. Confusion can therefore arise if those using the term generically have not grasped each other’s specific meanings.</p>
<p>In the context of ELIXIR, this situation came to the fore in preparations for the EXCELERATE project, whose training programme (WP11) includes an explicit e-learning subtask (11.1.3) as part of the commitment to build an ELIXIR training infrastructure. The ultimate deliverable of the subtask is to develop an ELIXIR e-learning policy and deploy e-learning platform(s) at the ELIXIR level. But what does an ‘<em>e-learning platform for ELIXIR</em>’ mean? Is it an instance of a <strong>MOOC platform</strong>, a customised LMS, a bespoke VLE, an ER repository, an aggregator, or something else? Clarification of this question was important, because each of the possible answers has very different implementation and resource requirements.</p>
<p>To try to address this question, and to facilitate communication both within ELIXIR, and between the ELIXIR and GOBLET trainer communities, an initial workshop – <em>Defining an e-learning lingua franca</em> – was held in Ljubljana (SI), 15-17 September 2015. At one level, the aim was to develop an overview of some of the e-learning approaches and applications developed or used by representatives from ELIXIR, GOBLET and other organisations – participants were therefore asked briefly to describe the systems they’d developed, to allow them, and their respective strengths and weaknesses, to be compared. At another level, the aim of the workshop was to try to converge on a common e-learning ‘language’, to help the ELIXIR and GOBLET trainer communities to communicate more coherently. To broaden the picture and gain a wider understanding of the challenges, a follow-up event was held during the GOBLET Annual General Meeting in Cape Town (ZA), 18-20 November 2015. Here, the outcomes of the first meeting were further discussed and refined.</p>
<p>Gaining a clearer view of the current e-learning landscape, and consensus on what we collectively mean by e-learning, were the necessary first steps towards formulating appropriate e-learning strategies for ELIXIR and GOBLET, and suggesting solutions that can feasibly be implemented. In the event, the issues were more deep-rooted than we expected, and many additional discussions were needed. This paper reflects the results of those discussions and of the deliberations of the workshop participants.</p>
https://doi.org/10.5281/zenodo.166378
oai:zenodo.org:166378
Zenodo
https://zenodo.org/communities/sib-training
https://zenodo.org/communities/dtl
https://zenodo.org/communities/goblet
https://zenodo.org/communities/elixir
https://zenodo.org/communities/eu
https://doi.org/
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
e-learning
training
bioinformatics
educational resource
Learning-Management Systems
Content-Management Systems
MOOC
Defining a lingua franca for the ELIXIR/GOBLET e-learning ecosystem
info:eu-repo/semantics/report
oai:zenodo.org:7723255
2023-03-11T17:59:51Z
user-goblet
Meeta Mistry
Shannan Ho Sui
Jihe Liu
Mary Piper
William Gammerdinger
Radhika Khetani
2023-03-11
<p>Second release of the ChIP-seq data analysis training materials from the Harvard Chan Bioinformatics Core (<a href="https://bioinformatics.sph.harvard.edu/training">https://bioinformatics.sph.harvard.edu/training</a>). The raw data was obtained from the SRA (<a href="https://www.ncbi.nlm.nih.gov/sra?term=SRP134733">https://www.ncbi.nlm.nih.gov/sra?term=SRP134733</a>).</p>
<p>Learning Objectives</p>
<ul>
<li>Understand the necessity for, and use of, the command line interface (bash) and HPC for analyzing high-throughput sequencing data.</li>
<li>Understand best practices for designing a ChIP-seq experiment and analysis the resulting data.</li>
</ul>
<p>Description This workshop focuses on teaching computational skills to enable the effective use of an high-performance computing environment to implement a ChIP-seq data analysis workflow. In addition to running the workflow from FASTQ files to peak calls, the workshop covers best practice guidelines for ChIP-seq experimental design and data organization/management and data visualization for quality control. Comparison with ATAC-seq and CUT&RUN methods were included in 2022.</p>
<ul>
<li>Introduction to ChIP-seq</li>
<li>QC using FASTQC</li>
<li>Alignment and filtering of reads (Bowtie2, Samtools)</li>
<li>Peak calling (MACS2)</li>
<li>Peak overlap (bedtools)</li>
<li>Peak visualization (using deepTools)</li>
</ul>
https://doi.org/10.5281/zenodo.7723255
oai:zenodo.org:7723255
Zenodo
https://github.com/hbctraining/Intro-to-ChIPseq-flipped/tree/chip-seq
https://zenodo.org/communities/goblet
https://doi.org/10.5281/zenodo.5825870
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
chip-seq, macs2, atac-seq, cut&run
hbctraining/Intro-to-ChIPseq-flipped: Understanding Chromatin Biology - Lessons from HCBC (2nd release)
info:eu-repo/semantics/lecture