Materials - TeSS Sandbox (Training eSupport System)

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- Scientific topic
- Data management106
- Metadata management106
- Research data management (RDM)106
- Algorithms89
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- Exomes64
- Genome annotation64
- Genomes64
- Genomics64
- Personal genomics64
- Synthetic genomics64
- Viral genomics64
- Whole genomes64
- Bottom-up proteomics53
- Discovery proteomics53
- MS-based targeted proteomics53
- MS-based untargeted proteomics53
- Metaproteomics53
- Peptide identification53
- Protein and peptide identification53
- Proteomics53
- Quantitative proteomics53
- Targeted proteomics53
- Top-down proteomics53
- Bayesian methods51
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- Markov processes51
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- Probability51
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- Statistics and probability51
- Community analysis46
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- Microbiome46
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- FAIR data44
- Findable, accessible, interoperable, reusable data44
- Metagenomics44
- Shotgun metagenomics44
- Biological sequences42
- Sequence analysis42
- Sequence databases42
- Comparative transcriptomics39
- Transcriptome39
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- Antimicrobial stewardship36
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- Assembly29
- Sequence assembly29
- Rare diseases28
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- Ecological informatics27
- Ecology27
- Ecosystem science27
- Protein bioinformatics26
- Protein databases26
- Protein informatics26
- Proteins26
- Biomathematics25
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- Protein structure25
- Protein structure analysis25
- Protein tertiary structure25
- Theoretical biology25
- Diffraction experiment24
- Imaging24
- Microscopy24
- Microscopy imaging24
- Optical super resolution microscopy24
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- Photonic microscopy24
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- MS-based targeted metabolomics22
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- Operation
- Data handling48
- File handling48
- File processing48
- Processing48
- Report handling48
- Utility operation48
- Data extraction13
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- 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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- Tool
- Galaxy334
- FastQC33
- SAMtools27
- MultiQC24
- Bioconductor23
- BWA20
- fastp18
- BEDTools16
- scikit-learn15
- Cutadapt14
- Data Stewardship Wizard14
- JBrowse14
- SCANPY14
- BLAST12
- DeepTools12
- STAR11
- BUSCO10
- Falco10
- QUAST10
- ggplot210
- taxonomy_krona_chart10
- FreeBayes9
- GEMINI9
- Trimmomatic9
- scikit-image9
- FASTX-Toolkit8
- Galaxy Image Analysis8
- NanoPlot8
- kraken28
- BCFtools7
- BamTools7
- HISAT27
- RStudio7
- msConvert7
- Bandage6
- Biopython6
- Bowtie 26
- MAFFT6
- MaxQuant6
- Open Babel6
- Workflow4Metabolomics6
- gffread6
- seqtk6
- Flye5
- Galactic Circos5
- MetaPhlAn5
- Minimap25
- MuSiC suite: PoPMuSiC, HoTMuSiC, and SNPMuSiC5
- RSeQC5
- StringTie5
- Trim Galore5
- 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
- UniProt4
- anndata4
- bx-python4
- mothur4
- pyGenomeTracks4
- snpEff4
- Apollo3
- Bracken3
- BridgeDb3
- BridgeDbR3
- Cardinal3
- CellProfiler3
- Clustal 1.8 (Clustal W, Clustal X)3
- DESeq23
- 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
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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 Training701
- European Bioinformatics Institute (EBI)479
- GOBLET108
- Swiss Institute of Bioinformatics80
- Software Carpentry70
- Finn's Test Provider53
- 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
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- 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
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- Bioconductor-Test1
- Biomedical Sciences Research Center "Alexander Fleming"1
- Future Learn1
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- UCLouvain Bioinformatics Platform1
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- Keyword
- training64
- Galaxy Server administration57
- jupyter-notebook55
- Foundations of Data Science50
- biodiversity43
- data management41
- Proteomics40
- Single Cell40
- Statistics and machine learning39
- microgalaxy39
- Transcriptomics29
- FAIR28
- Genome Annotation28
- Ecology27
- Rare Diseases & Research27
- Using Galaxy and Managing your Data27
- Contributing to the Galaxy Training Material26
- Microbiome26
- Bioinformatics25
- Development in Galaxy25
- Assembly22
- Data analysis20
- FAIR Data, Workflows, and Research20
- FAIR data20
- ansible19
- data stewardship19
- genes and genomes19
- DNA RNA18
- Variant Analysis18
- git-gat18
- interactive-tools18
- Imaging17
- Teaching and Hosting Galaxy training17
- elixir17
- work-in-progress17
- Climate16
- Python16
- Roslin Institute16
- Sequence analysis16
- jbrowse116
- life-sciences16
- reproducibility16
- Ontologies15
- earth-system15
- fair15
- transcriptomics15
- Introduction to Galaxy Analyses14
- Programming14
- gmod14
- Data management planning13
- Babraham Institute13
- Epigenetics13
- Proteins13
- R13
- Shell13
- data visualisation13
- medicine and health13
- next generation sequencing13
- programming13
- prokaryote13
- EeLP12
- Metabolomics12
- eLearning12
- health-informatics12
- paper-replication12
- Chemical biology11
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- Europe PMC11
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- biostatistics11
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- covid1910
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- Difficulty level
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- Licence
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- Creative Commons Attribution 4.0 International706
- Creative Commons Attribution Share Alike 4.0 International47
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- Creative Commons Attribution Non Commercial 4.0 International6
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- GNU General Public License v3.0 only5
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- Target audience
- Students479
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- Beginners15
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- data stewards11
- health professionals10
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- PhD8
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- programmers4
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- geneticists3
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- modelers3
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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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- data manager2
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- Terri Attwood18
- Wendi Bacon18
- The Gulbenkian Training Programme in Bioinformatics17
- Anne Fouilloux16
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- Maria Doyle14
- Martin Morgan14
- Donny Vrins13
- Geert van Geest13
- James Johnson13
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- Korbinian Bösl7
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- Laura Leroi7
- Martin Čech7
- Michael Charleston7
- Personalized Health Informatics Group7
- Praveen Kumar7
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- Andrew Mason6
- Anna Syme6
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- Saskia Hiltemann523
- Helena Rasche466
- Björn Grüning387
- Bérénice Batut228
- Nicola Soranzo147
- Martin Čech113
- Anthony Bretaudeau103
- Cristóbal Gallardo95
- Niall Beard81
- Wendi Bacon72
- Nate Coraor61
- Armin Dadras60
- Gildas Le Corguillé57
- Marius van den Beek55
- William Durand55
- Mehmet Tekman44
- Teresa Müller44
- Simon Gladman43
- Lucille Delisle41
- Pavankumar Videm37
- Yvan Le Bras37
- Wolfgang Maier36
- Melanie Föll34
- Beatriz Serrano-Solano32
- Simon Bray28
- Anup Kumar26
- Subina Mehta25
- Donny Vrins24
- Maria Doyle23
- Peter van Heusden23
- Anne Fouilloux20
- Julia Jakiela20
- Bazante Sanders19
- Anton Nekrutenko17
- Khaled Jum'ah17
- Deepti Varshney16
- Marie Josse14
- Mélanie Petera14
- Pratik Jagtap13
- Timothy J. Griffin13
- Matthias Bernt12
- Mira Kuntz12
- Pablo Moreno12
- Paul Zierep12
- David López11
- Delphine Lariviere11
- Katarzyna Kamieniecka11
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- Gianmauro Cuccuru10
- Leonid Kostrykin10
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- Coline Royaux4
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- Mateusz Kuzak4
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- Associated Training Datasets363
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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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- training2
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