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data/ara_automated_record_analysis/ara_automated_record_analysis.biotools.json
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| { | ||
| "accessibility": "Open access", | ||
| "additionDate": "2023-07-29T10:54:09.924115Z", | ||
| "biotoolsCURIE": "biotools:ara_automated_record_analysis", | ||
| "biotoolsID": "ara_automated_record_analysis", | ||
| "cost": "Free of charge", | ||
| "credit": [ | ||
| { | ||
| "email": "[email protected]", | ||
| "name": "Anand Maurya", | ||
| "note": "Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland", | ||
| "orcidid": "https://orcid.org/0000-0002-6204-2164", | ||
| "typeEntity": "Person", | ||
| "typeRole": [ | ||
| "Developer" | ||
| ] | ||
| }, | ||
| { | ||
| "email": "[email protected]", | ||
| "name": "Maciej Szymanski", | ||
| "note": "Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland", | ||
| "typeEntity": "Person", | ||
| "typeRole": [ | ||
| "Contributor" | ||
| ] | ||
| }, | ||
| { | ||
| "email": "[email protected]", | ||
| "name": "Wojciech Karlowski", | ||
| "note": "Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland", | ||
| "typeEntity": "Person", | ||
| "typeRole": [ | ||
| "Primary contact" | ||
| ] | ||
| } | ||
| ], | ||
| "description": "An automatic pipeline for exploration of SRA datasets with sequences as a query", | ||
| "documentation": [ | ||
| { | ||
| "type": [ | ||
| "User manual" | ||
| ], | ||
| "url": "https://github.com/maurya-anand/ARA/blob/main/README.md" | ||
| } | ||
| ], | ||
| "download": [ | ||
| { | ||
| "type": "Source code", | ||
| "url": "https://github.com/maurya-anand/ARA", | ||
| "version": "1.6.0" | ||
| } | ||
| ], | ||
| "editPermission": { | ||
| "type": "private" | ||
| }, | ||
| "function": [ | ||
| { | ||
| "cmd": "perl ara.pl --help", | ||
| "input": [ | ||
| { | ||
| "data": { | ||
| "term": "Nucleic acid sequence", | ||
| "uri": "http://edamontology.org/data_2977" | ||
| }, | ||
| "format": [ | ||
| { | ||
| "term": "Textual format", | ||
| "uri": "http://edamontology.org/format_2330" | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "note": "The tool requires a fasta file and SRA run accession as input.", | ||
| "operation": [ | ||
| { | ||
| "term": "Sequence alignment", | ||
| "uri": "http://edamontology.org/operation_0292" | ||
| }, | ||
| { | ||
| "term": "Sequence annotation", | ||
| "uri": "http://edamontology.org/operation_0361" | ||
| }, | ||
| { | ||
| "term": "Sequence database search", | ||
| "uri": "http://edamontology.org/operation_0338" | ||
| }, | ||
| { | ||
| "term": "Sequence feature detection", | ||
| "uri": "http://edamontology.org/operation_0253" | ||
| } | ||
| ], | ||
| "output": [ | ||
| { | ||
| "data": { | ||
| "term": "Text data", | ||
| "uri": "http://edamontology.org/data_2526" | ||
| }, | ||
| "format": [ | ||
| { | ||
| "term": "Textual format", | ||
| "uri": "http://edamontology.org/format_2330" | ||
| } | ||
| ] | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "homepage": "https://github.com/maurya-anand/ARA", | ||
| "language": [ | ||
| "Perl" | ||
| ], | ||
| "lastUpdate": "2023-07-29T10:54:43.322863Z", | ||
| "license": "GPL-3.0", | ||
| "link": [ | ||
| { | ||
| "type": [ | ||
| "Repository" | ||
| ], | ||
| "url": "https://github.com/maurya-anand/ARA" | ||
| } | ||
| ], | ||
| "maturity": "Mature", | ||
| "name": "ARA (Automated Record Analysis)", | ||
| "operatingSystem": [ | ||
| "Linux", | ||
| "Mac" | ||
| ], | ||
| "owner": "maurya-anand", | ||
| "toolType": [ | ||
| "Command-line tool" | ||
| ], | ||
| "topic": [ | ||
| { | ||
| "term": "Bioinformatics", | ||
| "uri": "http://edamontology.org/topic_0091" | ||
| }, | ||
| { | ||
| "term": "Data identity and mapping", | ||
| "uri": "http://edamontology.org/topic_3345" | ||
| }, | ||
| { | ||
| "term": "Mapping", | ||
| "uri": "http://edamontology.org/topic_0102" | ||
| } | ||
| ], | ||
| "version": [ | ||
| "1.6.0" | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,104 @@ | ||
| { | ||
| "accessibility": "Open access", | ||
| "additionDate": "2023-07-26T14:53:27.004301Z", | ||
| "biotoolsCURIE": "biotools:callc", | ||
| "biotoolsID": "callc", | ||
| "cost": "Free of charge", | ||
| "credit": [ | ||
| { | ||
| "email": "[email protected]", | ||
| "name": "Robbin Bouwmeester", | ||
| "orcidid": "https://orcid.org/0000-0001-6807-7029" | ||
| } | ||
| ], | ||
| "description": "Retention time prediction of small molecules with generalized calibration.", | ||
| "download": [ | ||
| { | ||
| "type": "Downloads page", | ||
| "url": "https://github.com/compomics/CALLC/releases/latest", | ||
| "version": "latest" | ||
| } | ||
| ], | ||
| "editPermission": { | ||
| "type": "private" | ||
| }, | ||
| "function": [ | ||
| { | ||
| "input": [ | ||
| { | ||
| "data": { | ||
| "term": "Text data", | ||
| "uri": "http://edamontology.org/data_2526" | ||
| }, | ||
| "format": [ | ||
| { | ||
| "term": "CSV", | ||
| "uri": "http://edamontology.org/format_3752" | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "operation": [ | ||
| { | ||
| "term": "Prediction and recognition", | ||
| "uri": "http://edamontology.org/operation_2423" | ||
| } | ||
| ], | ||
| "output": [ | ||
| { | ||
| "data": { | ||
| "term": "Text data", | ||
| "uri": "http://edamontology.org/data_2526" | ||
| }, | ||
| "format": [ | ||
| { | ||
| "term": "CSV", | ||
| "uri": "http://edamontology.org/format_3752" | ||
| } | ||
| ] | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "homepage": "https://github.com/compomics/CALLC", | ||
| "lastUpdate": "2023-07-26T14:53:27.006748Z", | ||
| "license": "Apache-2.0", | ||
| "maturity": "Mature", | ||
| "name": "CALLC", | ||
| "operatingSystem": [ | ||
| "Linux", | ||
| "Mac", | ||
| "Windows" | ||
| ], | ||
| "owner": "robbin.bouwmeester", | ||
| "publication": [ | ||
| { | ||
| "doi": "10.1021/acs.analchem.0c00233", | ||
| "metadata": { | ||
| "abstract": "Accurate prediction of liquid chromatographic retention times from small-molecule structures is useful for reducing experimental measurements and for improved identification in targeted and untargeted MS. However, different experimental setups (e.g., differences in columns, gradients, solvents, or stationary phase) have given rise to a multitude of prediction models that only predict accurate retention times for a specific experimental setup. In practice this typically results in the fitting of a new predictive model for each specific type of setup, which is not only inefficient but also requires substantial prior data to be accumulated on each such setup. Here we introduce the concept of generalized calibration, which is capable of the straightforward mapping of retention time models between different experimental setups. This concept builds on the database-controlled calibration approach implemented in PredRet and fits calibration curves on predicted retention times instead of only on observed retention times. We show that this approach results in substantially higher accuracy of elution-peak prediction than is achieved by setup-specific models.", | ||
| "authors": [ | ||
| { | ||
| "name": "Bouwmeester R." | ||
| }, | ||
| { | ||
| "name": "Degroeve S." | ||
| }, | ||
| { | ||
| "name": "Martens L." | ||
| } | ||
| ], | ||
| "citationCount": 19, | ||
| "date": "2020-05-05T00:00:00Z", | ||
| "journal": "Analytical Chemistry", | ||
| "title": "Generalized Calibration across Liquid Chromatography Setups for Generic Prediction of Small-Molecule Retention Times" | ||
| }, | ||
| "pmid": "32281370", | ||
| "type": [ | ||
| "Primary" | ||
| ] | ||
| } | ||
| ], | ||
| "version": [ | ||
| "v1.0" | ||
| ] | ||
| } |
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