Materials - TeSS Sandbox (Training eSupport System)

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- Scientific topic
- Data management105
- Metadata management105
- Research data management (RDM)105
- Algorithms89
- Computer programming89
- Data structures89
- Programming languages89
- Software development89
- Software engineering89
- Exomes63
- Genome annotation63
- Genomes63
- Genomics63
- Personal genomics63
- Synthetic genomics63
- Viral genomics63
- Whole genomes63
- Bottom-up proteomics58
- Discovery proteomics58
- MS-based targeted proteomics58
- MS-based untargeted proteomics58
- Metaproteomics58
- Peptide identification58
- Protein and peptide identification58
- Proteomics58
- Quantitative proteomics58
- Targeted proteomics58
- Top-down proteomics58
- Bayesian methods47
- Biostatistics47
- Descriptive statistics47
- Gaussian processes47
- Inferential statistics47
- Markov processes47
- Multivariate statistics47
- Probabilistic graphical model47
- Probability47
- Statistics47
- Statistics and probability47
- FAIR data44
- Findable, accessible, interoperable, reusable data44
- Biological sequences41
- Sequence analysis41
- Sequence databases41
- Community analysis39
- Comparative transcriptomics39
- Environmental microbiology39
- Microbial ecology39
- Microbiome39
- Molecular community analysis39
- Transcriptome39
- Transcriptomics39
- Metagenomics37
- Shotgun metagenomics37
- Antimicrobial stewardship36
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- Microbial physiology36
- Microbial surveillance36
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- Bioinformatics31
- DNA variation30
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- Somatic mutations30
- Assembly28
- Rare diseases28
- Sequence assembly28
- Computational ecology27
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- Ecological informatics27
- Ecology27
- Ecosystem science27
- Protein bioinformatics26
- Protein databases26
- Protein informatics26
- Proteins26
- Biomathematics25
- Computational biology25
- Mathematical biology25
- Protein structure25
- Protein structure analysis25
- Protein tertiary structure25
- Theoretical biology25
- Exometabolomics22
- LC-MS-based metabolomics22
- MS-based metabolomics22
- MS-based targeted metabolomics22
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- Metabolites22
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- NMR-based metabolomics22
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- Operation
- Data handling48
- File handling48
- File processing48
- Processing48
- Report handling48
- Utility operation48
- Data extraction13
- Data retrieval13
- Data retrieval (metadata)13
- Metadata retrieval13
- Retrieval13
- Data analysis10
- Mathematical modelling8
- Modelling and simulation8
- Data brokering7
- Data deposition7
- Data deposition brokering7
- Data submission7
- Database deposition7
- Database submission7
- Data visualisation6
- Molecular visualisation6
- Plotting6
- Rendering6
- Visualisation6
- Database retrieval5
- Query5
- Query and retrieval5
- Annotation2
- Database search2
- Normalisation2
- Ontology browsing2
- Ontology visualisation2
- RNA-Seq analysis2
- Search2
- Standardisation2
- Standardisation and normalisation2
- Alignment1
- Alignment construction1
- Alignment generation1
- Allele calling1
- Biological network analysis1
- Biological network modelling1
- Biological network prediction1
- Comparison1
- Data editing1
- Data formatting1
- Data reformatting1
- Exome variant detection1
- File format conversion1
- File formatting1
- File reformatting1
- Format conversion1
- Genome variant detection1
- Germ line variant calling1
- Image analysis1
- Mutation detection1
- Network analysis1
- Network comparison1
- Network modelling1
- Network prediction1
- Network simulation1
- Network topology simulation1
- Quality control1
- Read pre-processing1
- Sequence generation1
- Sequence generation (nucleic acid)1
- Sequence generation (protein)1
- Sequence read pre-processing1
- Somatic variant calling1
- Validation1
- Variant calling1
- Variant mapping1
- de novo mutation detection1
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- Tool
- Galaxy324
- FastQC32
- SAMtools27
- Bioconductor23
- MultiQC22
- BWA20
- fastp17
- BEDTools15
- scikit-learn15
- Cutadapt14
- Data Stewardship Wizard14
- SCANPY14
- JBrowse13
- BLAST12
- DeepTools12
- QUAST10
- STAR10
- ggplot210
- BUSCO9
- Falco9
- FreeBayes9
- GEMINI9
- taxonomy_krona_chart9
- NanoPlot8
- Trimmomatic8
- kraken28
- BCFtools7
- BamTools7
- FASTX-Toolkit7
- Galaxy Image Analysis7
- HISAT27
- RStudio7
- msConvert7
- scikit-image7
- Bandage6
- Biopython6
- MAFFT6
- MaxQuant6
- Open Babel6
- Workflow4Metabolomics6
- seqtk6
- Bowtie 25
- Flye5
- Galactic Circos5
- MetaPhlAn5
- Minimap25
- MuSiC suite: PoPMuSiC, HoTMuSiC, and SNPMuSiC5
- RSeQC5
- StringTie5
- annotatemyids5
- compute_sequence_length5
- gffcompare5
- gffread5
- xcms5
- Bwa-mem24
- Chipster4
- Diamond4
- GOseq4
- KrakenTools4
- MACS4
- MSstats4
- Merqury4
- Newick Utilities4
- SRA Software Toolkit4
- The Protein Data Bank (PDB)4
- Trim Galore4
- UniProt4
- anndata4
- mothur4
- snpEff4
- Apollo3
- Bracken3
- BridgeDb3
- BridgeDbR3
- Cardinal3
- CellProfiler3
- Clustal 1.8 (Clustal W, Clustal X)3
- DISEASES3
- DropletUtils3
- FastTree3
- GenomeScope 2.03
- GraPhlAn3
- InterMine3
- InterMineR3
- InterProScan (EBI)3
- MGnify (was EBI Metagenomics)3
- Ontology Lookup Service3
- QualiMap3
- R3
- RDKit3
- Salmon3
- SeqCode3
- SortMeRNA3
- Stacks3
- UCSC Genome Browser Utilities3
- Unicycler3
- Unipept3
- Vcflib3
- bed to protein map3
- bx-python3
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- Standard database or policy
- Ensembl10
- Protein Data Bank in Europe5
- European Nucleotide Archive4
- NCBI Gene4
- ChEMBL: a large-scale bioactivity database for drug discovery3
- IntAct molecular interaction database3
- Integrated resource of protein families, domains and functional sites3
- ArrayExpress2
- EBI Metagenomics2
- Minimum Information about Plant Phenotyping Experiment2
- OBO Foundry2
- STRING: functional protein association networks2
- Search Tool for Interactions of Chemicals2
- eNanoMapper Ontology2
- Wheat Data Interoperability Guidelines 1
- A repository of mathematical models of biological and biomedical systems1
- BRENDA1
- Bioschemas1
- BridgeDb1
- Cellular Microscopy Phenotype Ontology1
- Chemical Entities of Biological Interest1
- Common Workflow Language1
- Crop Ontology1
- Europe PubMed Central1
- Expression Atlas1
- Gene Ontology1
- Gene3D1
- Genomics England | PanelApp1
- HumanMine1
- IUPAC International Chemical Identifier1
- Identifiers.org Registry1
- MDL molfile Format1
- MetaboLights1
- Multi-Crop Passport Descriptors1
- OMOP Common Data Model1
- Observational Medical Outcomes Partnership Standard Vocabulary1
- PRINTS1
- PRoteomics IDEntifications database1
- Plant Phenotype Experiment Ontology1
- Protein Data Bank: Proteins, Interfaces, Structures and Assemblies1
- ProteomeXchange1
- PubMed Central1
- Resource Description Framework1
- SUPERFAMILY1
- Schema.org1
- Simplified Molecular Input Line Entry Specification Format1
- Structural Classification Of Proteins1
- The European Genome-phenome Archive1
- The Human Metabolome Database1
- Variant Effect Predictor data format1
- Wheat Trait Ontology1
- Wikidata1
- data.eNanoMapper.net1
- i2b2-patient_visit_dimensions1
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- Content provider
- Galaxy Training688
- European Bioinformatics Institute (EBI)470
- GOBLET108
- Swiss Institute of Bioinformatics78
- Software Carpentry70
- Finn's Test Provider51
- DTLS - Dutch Techcentre For Life Sciences40
- Bioinformatics and Biomathematics Training Hub34
- Khan Academy Statistics32
- Bioconductor24
- ELIXIR Portugal20
- Coursera17
- CINECA PROJECT14
- ELIXIR Brazil14
- IFB French Institute of Bioinformatics10
- PerMedCoE10
- VIB Bioinformatics Core10
- eNanoMapper10
- Bioschemas9
- Data Carpentry9
- Genome 3D8
- CSC - IT Center for Science7
- Centre for Digital Life Norway7
- Department of Bioinformatics - BiGCaT, Maastricht University7
- InterMine7
- NanoCommons7
- Australian BioCommons6
- Data Steward team Ghent University6
- ELIXIR Luxembourg6
- ELIXIR Slovenia5
- ELIXIR-SI eLearning Platform (EeLP)5
- Barcelona Supercomputing Center (BSC)4
- EMBL-ABR4
- Proteomics Academy4
- University of Cambridge Bioinformatics Training4
- COG-Train3
- ELIXIR3
- Novo Nordisk Foundation Center for Protein Research3
- ELIXIR Norway2
- ELIXIR: The Czech Republic Node2
- Bioconductor-Test1
- Biomedical Sciences Research Center "Alexander Fleming"1
- Future Learn1
- NBIS1
- Open Science MOOC1
- Test Provider1
- UCLouvain Bioinformatics Platform1
- de.NBI1
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- Keyword
- training64
- Galaxy Server administration58
- jupyter-notebook55
- Foundations of Data Science51
- Proteomics45
- biodiversity42
- data management41
- Single Cell40
- microgalaxy39
- Statistics and machine learning35
- Transcriptomics29
- FAIR28
- Contributing to the Galaxy Training Material27
- Ecology27
- Genome Annotation27
- Rare Diseases & Research27
- Using Galaxy and Managing your Data27
- Bioinformatics25
- Development in Galaxy24
- Assembly22
- Data analysis20
- FAIR data20
- ansible20
- Microbiome19
- data stewardship19
- genes and genomes19
- interactive-tools19
- DNA RNA18
- FAIR Data, Workflows, and Research18
- Variant Analysis18
- git-gat18
- Teaching and Hosting Galaxy training17
- elixir17
- work-in-progress17
- Python16
- Roslin Institute16
- Sequence analysis16
- life-sciences16
- reproducibility16
- Climate15
- Imaging15
- Ontologies15
- fair15
- jbrowse115
- transcriptomics15
- Programming14
- earth-system14
- gmod14
- Data management planning13
- Babraham Institute13
- Epigenetics13
- Introduction to Galaxy Analyses13
- Proteins13
- R13
- Shell13
- data visualisation13
- medicine and health13
- next generation sequencing13
- programming13
- prokaryote13
- EeLP12
- Metabolomics12
- eLearning12
- health-informatics12
- paper-replication12
- Chemical biology11
- Data management plan11
- Europe PMC11
- Git11
- Introduction bioinformatics11
- MIGHTS11
- Metadata11
- ai-ml11
- biostatistics11
- cyoa11
- plants11
- workflows11
- Evolution10
- Extras10
- Gene Expression10
- HPC10
- Introduction10
- Literature search10
- Phylogenetics10
- covid1910
- eukaryote10
- label-free10
- mark ibberson group10
- services and resources10
- Computational chemistry9
- DDA9
- Genomics9
- Python biologists9
- Standards9
- bioinformatics9
- computer-science9
- machine learning9
- metadata9
- ocean9
- one-health9
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- Difficulty level
- Not specified1087
- Beginner749
- Intermediate197
- Advanced34
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- Licence
- License Not Specified1217
- Creative Commons Attribution 4.0 International693
- Creative Commons Attribution Share Alike 4.0 International47
- Creative Commons Attribution Non Commercial Share Alike 4.0 International24
- Creative Commons Attribution Non Commercial No Derivatives 4.0 International17
- Other (Not Open)16
- Other (Non-Commercial)14
- Creative Commons Attribution Non Commercial 4.0 International6
- Creative Commons Zero v1.0 Universal6
- MIT License6
- Apache License 2.05
- GNU General Public License v3.0 only5
- Other (Open)4
- GNU General Public License v2.0 only2
- Academic Free License v3.01
- BSD 3-Clause "New" or "Revised" License1
- Creative Commons Attribution No Derivatives 4.0 International1
- Other (Attribution)1
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- Target audience
- Students467
- Researchers203
- Biologists, Genomicists, Computer Scientists169
- Post-Doctoral Fellows162
- PhD students141
- Clinicians106
- Graduate students85
- Galaxy Administrators82
- Graduate Students78
- Instructors49
- Novice44
- Biologists38
- Life Science Researchers34
- bioinformaticians32
- PhD candidate27
- Intermediate26
- post-docs20
- Academia/ Research Institution17
- Industry17
- Non-Profit Organisation17
- life scientists16
- Beginners15
- Bench biologists15
- Healthcare15
- beginner bioinformaticians14
- Bioinformaticians13
- Trainers13
- software developers, bioinformaticians12
- data stewards11
- health professionals10
- Master students10
- PhD candidates9
- biocurators9
- healthcare professionals9
- Biomedical researchers8
- PhD8
- Biomedical Researchers7
- Data Managers7
- Data Scientists7
- Health Care Professionals7
- Research Scientists7
- Scientists7
- Training Designers7
- Training instructors7
- Patient Advocates 6
- Post Docs6
- rare disease patients representatives5
- All postgraduates5
- Anyone interested in simulation of metabolic models, and in PerMedCoE tools and activities5
- General Interest5
- Life scientists5
- Undergraduate students5
- biologists5
- computational scientists5
- data managers5
- postgrad5
- Chemists4
- Clinical Scientists4
- Computational biologists4
- Laboratory technicians4
- Professors4
- Veterinarians4
- postdocs4
- postdoctoral researchers4
- programmers4
- Life Scientists3
- Life scientists with programming skills3
- Postgraduate students3
- data steward / data manager3
- geneticists3
- medical students3
- modelers3
- plant researchers3
- postdoc3
- project manager3
- software engineers3
- teachers3
- Anyone interested in data standardization and/or the ontology approach (i.e. public, end users).2
- General Physicians2
- Life sciences2
- PhD Students2
- Staff2
- Technicians2
- biology and bioinformatics sophomore undergraduates2
- data manager2
- experimeintal biologist researchers2
- policy officer2
- scientific researchers, public health professionals and clinicians 2
- service administrators in organizations that want to make use of ELIXIR AAI 2
- statisticians2
- web developers2
- Research Assistants and Research Associates1
- Anyone1
- Anyone interested in bioinformatics1
- Anyone wants to start using the Unix/Linux OS1
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- Bachelor students1
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- Author
- Helena Rasche113
- SIB Swiss Institute of Bioinformatics103
- Bérénice Batut90
- Saskia Hiltemann55
- Björn Grüning38
- Anton Nekrutenko27
- bebatut27
- Anthony Bretaudeau26
- bgruening25
- Subina Mehta24
- The Carpentries23
- Yvan Le Bras22
- Fotis E. Psomopoulos21
- Michelle Brazas21
- Simon Gladman21
- Nicola Soranzo20
- Wandrille Duchemin20
- Nate Coraor19
- Bazante Sanders18
- Katarzyna Kamieniecka18
- Krzysztof Poterlowicz18
- Terri Attwood18
- Wendi Bacon18
- Marie Josse17
- The Gulbenkian Training Programme in Bioinformatics17
- Anne Fouilloux16
- Mehmet Tekman15
- Maria Doyle14
- Martin Morgan14
- Donny Vrins13
- Geert van Geest13
- James Johnson13
- Julia Jakiela13
- Katherine Do13
- Patricia Palagi13
- Wolfgang Maier13
- shiltemann13
- Cristóbal Gallardo12
- Egon Willighagen12
- Simon Andrews12
- Simon Bray12
- nekrut12
- Anup Kumar11
- Celia van Gelder11
- Delphine Lariviere11
- Khaled Jum'ah11
- Mathieu Bourgey11
- Melanie Föll11
- Pratik Jagtap11
- Dave Clements10
- Lucille Delisle10
- Mijke Jetten10
- Paul Yorke10
- Pavankumar Videm10
- Daniel Blankenberg9
- David Wishart9
- Jared Simpson9
- John Chilton9
- Marius van den Beek9
- allegra.via Via9
- Allegra Via8
- Anika Erxleben8
- Avans Hogeschool8
- Boris Steipe8
- Elisabeth Gasteiger8
- Helen Brown8
- Malachi Griffith8
- Maria Levchenko8
- Matthias Fahrner8
- Paul Zierep8
- Robin Engler8
- Stéphanie Robin8
- Timothy J. Griffin8
- Alex Ostrovsky7
- Alexander Botzki7
- Alexandre Cormier7
- Anne Pajon7
- Erwan Corre7
- Florian Christoph Sigloch7
- Joachim Wolff7
- Kaivan Kamali7
- Korbinian Bösl7
- Laura Cooper7
- Laura Leroi7
- Martin Čech7
- Michael Charleston7
- Personalized Health Informatics Group7
- Praveen Kumar7
- Robert Andrews7
- Sergio Martínez Cuesta7
- pajanne7
- stortebecker7
- Andrew Mason6
- Anna Syme6
- Branka Franicevic6
- Christopher Barnett6
- Coline Royaux6
- Dayane Araujo6
- ELIXIR Goblet Train the Trainers6
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- Contributor
- Saskia Hiltemann515
- Helena Rasche471
- Björn Grüning379
- Bérénice Batut232
- Nicola Soranzo148
- Martin Čech114
- Anthony Bretaudeau101
- Cristóbal Gallardo95
- Niall Beard81
- Wendi Bacon71
- Nate Coraor62
- Armin Dadras61
- Gildas Le Corguillé57
- Marius van den Beek55
- William Durand55
- Mehmet Tekman44
- Simon Gladman44
- Teresa Müller43
- Lucille Delisle42
- Yvan Le Bras37
- Pavankumar Videm36
- Wolfgang Maier35
- Melanie Föll34
- Beatriz Serrano-Solano32
- Simon Bray28
- Subina Mehta27
- Anup Kumar25
- Donny Vrins23
- Maria Doyle23
- Peter van Heusden23
- Anne Fouilloux20
- Julia Jakiela20
- Bazante Sanders19
- Anton Nekrutenko17
- Deepti Varshney16
- Khaled Jum'ah16
- Mélanie Petera14
- Pratik Jagtap13
- Timothy J. Griffin13
- Marie Josse12
- Matthias Bernt12
- Pablo Moreno12
- David López11
- Delphine Lariviere11
- Gianmauro Cuccuru11
- Marisa Loach11
- Mira Kuntz11
- Paul Zierep11
- Stéphanie Robin11
- Katarzyna Kamieniecka10
- Alexandre Cormier8
- Dave Clements8
- John Chilton8
- Leonid Kostrykin8
- Mallory Freeberg8
- Melissa Burke8
- Verena Moosmann8
- Daniel Sobral7
- Hans-Rudolf Hotz7
- Kaivan Kamali7
- Morgan Howells7
- Sabine Österle7
- Anna Syme6
- Bert Droesbeke6
- Christopher Barnett6
- Clemens Blank6
- Eija Korpelainen6
- Ekaterina Polkh6
- Enis Afgan6
- Florian Christoph Sigloch6
- Florian Heyl6
- Linelle Abueg6
- Tomas Klingström6
- Alex Ostrovsky5
- Alireza Khanteymoori5
- Clea Siguret5
- John Davis5
- Lieven Clement5
- Wandrille Duchemin5
- olisand5
- Catherine Bromhead4
- Coline Royaux4
- Dave B.4
- David Philip Judge4
- Diana Chiang Jurado4
- Eli Chadwick4
- Fotis E. Psomopoulos4
- Hélène Chiapello4
- Laura Leroi4
- Mateusz Kuzak4
- Phil Reed4
- Roland Krause4
- Romane LIBOUBAN4
- Solenne Correard4
- Amirhossein Naghsh Nilchi3
- Andrea Bagnacani3
- Daniel Faria3
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- slideck/ presentation4
- FREE online course3
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- online modules3
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- API reference2
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- Life Sciences Literature Database2
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- Mock data2
- Vignette2
- Carpentries style curriculum1
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- Related resource
- Associated Training Datasets354
- Associated Workflows276
- Quarto/RMarkdown Notebook185
- Jupyter Notebook (with Solutions)52
- Jupyter Notebook (without Solutions)52
- Input datasets32
- ansible19
- git-gat18
- Research Data Management in Life Sciences11
- Associated slides9
- Proteomics dataset5
- Sequence analysis dataset5
- Transcriptomics dataset5
- jobs5
- Assembly dataset4
- Variant Analysis dataset4
- Assembly slides3
- DMPonline3
- Data Stewardship Wizard3
- Development in Galaxy slides3
- Slides3
- Workshop recording3
- deploying3
- monitoring3
- ro-crate3
- ChIP-Seq data analysis dataset2
- Epigenetics dataset2
- Genome Annotation dataset2
- Metagenomics dataset2
- Sequence analysis slides2
- collections2
- cyoa2
- kubernetes2
- networking2
- storage2
- training2
- wireguard2
- workflows2
- ARROWSMITH1
- COBRA Toolbox1
- CanCOGeN1
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- DDA1
- DS Wizard ELIXIR-Norway 1
- ENA1
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- Galaxy project guided tours1
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- Genomics England PanelApp1
- Introduction to Galaxy Analyses dataset1
- Introduction to Galaxy dataset1
- Next generation biobanking ontology (NGBO)1
- Public Health Alliance for Genomic Epidemiology1
- RCN Open data policy 1
- RDMkit 1
- Ready For BioData Management?1
- SIG1
- Statistics dataset1
- TeSS GitHub1
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- Transcriptomics slides1
- User Interface and Features dataset1
- Workshop FAIR & Data stewardship for the 2020 ITN ProEVLifeCycle1
- Workshop FAIR & Data stewardship for the 2021 ITN ProEVLifeCycle1
- apollo21
- authentication1
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