Materials - TeSS Sandbox (Training eSupport System)

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- Data management99
- Metadata management99
- Research data management (RDM)99
- Algorithms87
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- Bottom-up proteomics48
- Discovery proteomics48
- MS-based targeted proteomics48
- MS-based untargeted proteomics48
- Metaproteomics48
- Peptide identification48
- Protein and peptide identification48
- Proteomics48
- Quantitative proteomics48
- Targeted proteomics48
- Top-down proteomics48
- FAIR data43
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- Biological sequences38
- Community analysis38
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- Microbial ecology38
- Microbiome38
- Molecular community analysis38
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- Sequence databases38
- Comparative transcriptomics37
- Transcriptome37
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- Metagenomics36
- Shotgun metagenomics36
- Exomes34
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- Genomes34
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- Proteins27
- Assembly26
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- Biomathematics25
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- Protein structure24
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- Protein tertiary structure24
- Computational ecology23
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- Ecological informatics23
- Ecology23
- Ecosystem science23
- Exometabolomics21
- LC-MS-based metabolomics21
- MS-based metabolomics21
- MS-based targeted metabolomics21
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- Metabolites21
- Metabolome21
- Metabolomics21
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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
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- de novo mutation detection1
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- Tool
- Galaxy285
- FastQC34
- SAMtools27
- Bioconductor23
- BWA19
- MultiQC18
- BEDTools16
- fastp16
- Cutadapt14
- Data Stewardship Wizard14
- scikit-learn14
- SCANPY13
- DeepTools12
- JBrowse12
- QUAST10
- BLAST9
- GEMINI9
- taxonomy_krona_chart9
- BUSCO8
- NanoPlot8
- STAR8
- Trimmomatic8
- kraken28
- FreeBayes7
- RStudio7
- BCFtools6
- Bandage6
- FASTX-Toolkit6
- MaxQuant6
- Open Babel6
- Workflow4Metabolomics6
- ggplot26
- msConvert6
- seqtk6
- BamTools5
- Bowtie 25
- Flye5
- Galactic Circos5
- HISAT25
- MSstats5
- MetaPhlAn5
- RSeQC5
- xcms5
- Biopython4
- Chipster4
- Diamond4
- HUMAnN24
- KrakenTools4
- MACS4
- MAFFT4
- Merqury4
- Minimap24
- MuSiC suite: PoPMuSiC, HoTMuSiC, and SNPMuSiC4
- Newick Utilities4
- The Protein Data Bank (PDB)4
- UniProt4
- annotatemyids4
- gffread4
- mothur4
- snpEff4
- Apollo3
- Bracken3
- BridgeDb3
- BridgeDbR3
- Bwa-mem23
- Cardinal3
- CellProfiler3
- Clustal 1.8 (Clustal W, Clustal X)3
- DISEASES3
- DropletUtils3
- GOseq3
- Galaxy Image Analysis3
- GenomeScope 2.03
- GraPhlAn3
- InterMine3
- InterMineR3
- InterProScan (EBI)3
- MGnify (was EBI Metagenomics)3
- Ontology Lookup Service3
- QualiMap3
- RDKit3
- SeqCode3
- SortMeRNA3
- Stacks3
- Unicycler3
- Unipept3
- bx-python3
- compute_sequence_length3
- export2graphlan3
- gfastats3
- gffcompare3
- humann3
- lofreq3
- pyGenomeTracks3
- scikit-image3
- snippy3
- Bakta2
- Bio3D2
- COBREXA.jl2
- COMBAT-TB Workbench2
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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 Training626
- European Bioinformatics Institute (EBI)451
- GOBLET108
- Swiss Institute of Bioinformatics72
- Software Carpentry70
- Finn's Test Provider44
- DTLS - Dutch Techcentre For Life Sciences40
- Bioinformatics and Biomathematics Training Hub34
- Khan Academy Statistics32
- Bioconductor24
- ELIXIR Portugal20
- Coursera17
- CINECA PROJECT14
- ELIXIR Brazil13
- 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
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- NBIS1
- Open Science MOOC1
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- UCLouvain Bioinformatics Platform1
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- Keyword
- training58
- Galaxy Server administration54
- Foundations of Data Science50
- jupyter-notebook46
- data management41
- Single Cell36
- microgalaxy36
- Proteomics35
- Transcriptomics28
- FAIR27
- Rare Diseases & Research27
- Bioinformatics25
- Contributing to the Galaxy Training Material25
- Using Galaxy and Managing your Data25
- Development in Galaxy24
- Ecology23
- Genome Annotation23
- Assembly21
- Statistics and machine learning21
- Data analysis20
- FAIR data20
- FAIR Data, Workflows, and Research19
- ansible19
- data stewardship19
- DNA RNA18
- Microbiome18
- Python18
- git-gat18
- interactive-tools18
- Teaching and Hosting Galaxy training17
- Variant Analysis17
- genes and genomes17
- 10x16
- Roslin Institute16
- life-sciences16
- reproducibility16
- Ontologies15
- R15
- fair15
- Climate14
- Introduction to Galaxy Analyses14
- Programming14
- Sequence analysis14
- gmod14
- jbrowse114
- Data management planning13
- Babraham Institute13
- Epigenetics13
- Proteins13
- Shell13
- data visualisation13
- earth-system13
- programming13
- prokaryote13
- EeLP12
- eLearning12
- health-informatics12
- paper-replication12
- transcriptomics12
- Chemical biology11
- Data management plan11
- Europe PMC11
- Git11
- Imaging11
- Introduction bioinformatics11
- MIGHTS11
- Metabolomics11
- Metadata11
- biostatistics11
- cyoa11
- next generation sequencing11
- Extras10
- Gene Expression10
- HPC10
- Introduction10
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- Phylogenetics10
- covid1910
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- workflows10
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- Python biologists9
- Standards9
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- computer-science9
- metadata9
- one-health9
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- Difficulty level
- Not specified1065
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- Licence
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- Creative Commons Attribution 4.0 International633
- 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
- Students415
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- Biologists38
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- bioinformaticians32
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- Intermediate26
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- Academia/ Research Institution17
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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
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- Anyone interested in simulation of metabolic models, and in PerMedCoE tools and activities5
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- programmers4
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- geneticists3
- medical students3
- modelers3
- plant researchers3
- postdoc3
- project manager3
- software engineers3
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- 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
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- Author
- Helena Rasche111
- SIB Swiss Institute of Bioinformatics90
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- Marie Josse17
- The Gulbenkian Training Programme in Bioinformatics17
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- Mehmet Tekman15
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- Maria Doyle14
- Martin Morgan14
- Donny Vrins13
- Julia Jakiela13
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- Alex Ostrovsky7
- Alexander Botzki7
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- 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
- Stéphanie Robin7
- pajanne7
- stortebecker7
- Andrew Mason6
- Anna Syme6
- Branka Franicevic6
- Christopher Barnett6
- Coline Royaux6
- Dayane Araujo6
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- Saskia Hiltemann481
- Helena Rasche466
- Björn Grüning329
- Bérénice Batut206
- Nicola Soranzo145
- Anthony Bretaudeau96
- Cristóbal Gallardo94
- Niall Beard80
- Martin Čech69
- Nate Coraor62
- Gildas Le Corguillé57
- Marius van den Beek55
- Wendi Bacon54
- William Durand54
- Mehmet Tekman44
- Simon Gladman44
- Lucille Delisle41
- Melanie Föll34
- Yvan Le Bras33
- Pavankumar Videm29
- Beatriz Serrano-Solano28
- Simon Bray28
- Teresa Müller28
- Wolfgang Maier25
- Donny Vrins24
- Maria Doyle23
- Peter van Heusden23
- Subina Mehta21
- Julia Jakiela20
- Anne Fouilloux19
- Bazante Sanders19
- Anton Nekrutenko17
- Anup Kumar16
- Khaled Jum'ah16
- Deepti Varshney15
- Mélanie Petera14
- Marie Josse13
- Matthias Bernt12
- Pablo Moreno12
- David López11
- Mira Kuntz11
- Stéphanie Robin11
- Gianmauro Cuccuru10
- Marisa Loach10
- Delphine Lariviere9
- John Chilton9
- Katarzyna Kamieniecka9
- Dave Clements8
- Mallory Freeberg8
- Melissa Burke8
- Paul Zierep8
- Alexandre Cormier7
- Daniel Sobral7
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- Kaivan Kamali7
- Sabine Österle7
- Anna Syme6
- Bert Droesbeke6
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- Florian Christoph Sigloch6
- Florian Heyl6
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- Tomas Klingström6
- Alex Ostrovsky5
- Alireza Khanteymoori5
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- Lieven Clement5
- Pratik Jagtap5
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- Clea Siguret4
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- Daniel Faria3
- Daniel Neves3
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- Gautier Sarah3
- Janick Mathys3
- Jasper Ouwerkerk3
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- Jennifer Hillman-Jackson3
- Joachim Wolff3
- Krzysztof Poterlowicz3
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- Related resource
- Associated Training Datasets323
- Associated Workflows247
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- Jupyter Notebook (with Solutions)41
- Jupyter Notebook (without Solutions)41
- 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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- deploying3
- monitoring3
- ro-crate3
- ChIP-Seq data analysis dataset2
- Epigenetics dataset2
- Genome Annotation dataset2
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- Sequence analysis slides2
- collections2
- cyoa2
- kubernetes2
- networking2
- storage2
- training2
- wireguard2
- workflows2
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- Introduction to Galaxy dataset1
- Next generation biobanking ontology (NGBO)1
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- Workshop FAIR & Data stewardship for the 2021 ITN ProEVLifeCycle1
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