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
- Exomes64
- Genome annotation64
- Genomes64
- Genomics64
- Personal genomics64
- Synthetic genomics64
- Viral genomics64
- Whole genomes64
- 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 genetics36
- Microbial physiology36
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- Microbiology36
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- Molecular microbiology36
- Bioinformatics31
- DNA variation30
- Genetic variation30
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- Somatic mutations30
- Assembly29
- Sequence assembly29
- Rare diseases28
- Computational ecology27
- Ecoinformatics27
- 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
- Diffraction experiment22
- Exometabolomics22
- Imaging22
- LC-MS-based metabolomics22
- MS-based metabolomics22
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- MS-based untargeted metabolomics22
- Mass spectrometry-based metabolomics22
- Metabolites22
- Metabolome22
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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
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- Sequence read pre-processing1
- Somatic variant calling1
- Validation1
- Variant calling1
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- de novo mutation detection1
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- Tool
- Galaxy325
- FastQC32
- SAMtools27
- Bioconductor23
- MultiQC22
- BWA20
- fastp17
- BEDTools15
- scikit-learn15
- Cutadapt14
- Data Stewardship Wizard14
- JBrowse14
- SCANPY14
- BLAST12
- DeepTools12
- STAR11
- BUSCO10
- QUAST10
- ggplot210
- 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
- gffread6
- seqtk6
- Bowtie 25
- Flye5
- Galactic Circos5
- MetaPhlAn5
- Minimap25
- MuSiC suite: PoPMuSiC, HoTMuSiC, and SNPMuSiC5
- RSeQC5
- StringTie5
- annotatemyids5
- compute_sequence_length5
- gffcompare5
- 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
- OMArk3
- Ontology Lookup Service3
- QualiMap3
- R3
- RDKit3
- Salmon3
- SeqCode3
- SortMeRNA3
- Stacks3
- UCSC Genome Browser Utilities3
- Unicycler3
- Unipept3
- Vcflib3
- bed to protein map3
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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 Training689
- European Bioinformatics Institute (EBI)472
- GOBLET108
- Swiss Institute of Bioinformatics79
- 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
- training70
- Galaxy Server administration58
- jupyter-notebook55
- Foundations of Data Science50
- Proteomics45
- biodiversity43
- data management42
- Single Cell40
- microgalaxy39
- Statistics and machine learning35
- Transcriptomics29
- FAIR28
- Genome Annotation28
- Contributing to the Galaxy Training Material27
- Ecology27
- Rare Diseases & Research27
- Using Galaxy and Managing your Data27
- Bioinformatics25
- Development in Galaxy24
- Assembly22
- Data analysis20
- FAIR data20
- ansible20
- genes and genomes20
- Microbiome19
- data stewardship19
- interactive-tools19
- DNA RNA18
- FAIR Data, Workflows, and Research18
- Variant Analysis18
- git-gat18
- Teaching and Hosting Galaxy training17
- elixir17
- reproducibility17
- work-in-progress17
- Python16
- Roslin Institute16
- Sequence analysis16
- jbrowse116
- life-sciences16
- programming16
- Climate15
- Imaging15
- Ontologies15
- fair15
- transcriptomics15
- Introduction to Galaxy Analyses14
- Programming14
- data visualisation14
- earth-system14
- gmod14
- Data management planning13
- Babraham Institute13
- Epigenetics13
- Proteins13
- R13
- Shell13
- biostatistics13
- medicine and health13
- next generation sequencing13
- prokaryote13
- EeLP12
- Metabolomics12
- eLearning12
- health-informatics12
- paper-replication12
- Chemical biology11
- Data management plan11
- Europe PMC11
- Git11
- Introduction bioinformatics11
- MIGHTS11
- Metadata11
- ai-ml11
- cyoa11
- mark ibberson group11
- plants11
- torsten schwede & thierry sengstag group11
- workflows11
- Evolution10
- Extras10
- Gene Expression10
- HPC10
- Introduction10
- Literature search10
- Phylogenetics10
- covid1910
- eukaryote10
- label-free10
- machine learning10
- services and resources10
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- DDA9
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- Python biologists9
- Standards9
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- Difficulty level
- Not specified1089
- Beginner750
- Intermediate198
- Advanced34
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- Licence
- License Not Specified1220
- Creative Commons Attribution 4.0 International694
- 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
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- Target audience
- Students468
- Researchers203
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- Post-Doctoral Fellows162
- PhD students141
- Clinicians106
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- Graduate Students78
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- Biologists38
- Life Science Researchers34
- bioinformaticians32
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- Intermediate26
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- Academia/ Research Institution17
- Industry17
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- 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
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- All postgraduates5
- Anyone interested in simulation of metabolic models, and in PerMedCoE tools and activities5
- General Interest5
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- biologists5
- computational scientists5
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- Laboratory technicians4
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- postdocs4
- postdoctoral researchers4
- programmers4
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- 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
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- biology and bioinformatics sophomore undergraduates2
- data manager2
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- Anyone1
- Anyone interested in bioinformatics1
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- Author
- Helena Rasche113
- SIB Swiss Institute of Bioinformatics104
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- 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
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- Khaled Jum'ah11
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- Dave Clements10
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- Elisabeth Gasteiger8
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- Stéphanie Robin8
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- Alex Ostrovsky7
- Alexander Botzki7
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- Erwan Corre7
- Florian Christoph Sigloch7
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- 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
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- Saskia Hiltemann516
- Helena Rasche471
- Björn Grüning384
- Bérénice Batut232
- Nicola Soranzo148
- Martin Čech114
- Anthony Bretaudeau102
- 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 Vrins24
- 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
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- Morgan Howells7
- Sabine Österle7
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- 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
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- Lieven Clement5
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- Coline Royaux4
- Daniela Schneider4
- 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
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- Associated Training Datasets355
- Associated Workflows277
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- 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
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- Variant Analysis dataset4
- Assembly slides3
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- ChIP-Seq data analysis dataset2
- Epigenetics dataset2
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- collections2
- cyoa2
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- storage2
- training2
- wireguard2
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- Introduction to Galaxy dataset1
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- Workshop FAIR & Data stewardship for the 2021 ITN ProEVLifeCycle1
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