List all resources, or create a new resource.

GET /api/t/?documentationType=Manual
HTTP 200 OK
Allow: GET, POST, HEAD, OPTIONS
Content-Type: application/json
Vary: Accept

{
    "count": 2852,
    "previous": null,
    "list": [
        {
            "collectionID": [
                "IOCB CAS CZ"
            ],
            "accessibility": [
                "Open access"
            ],
            "topic": [
                {
                    "term": "Compound libraries and screening",
                    "uri": "http://edamontology.org/topic_3343"
                },
                {
                    "term": "Cheminformatics",
                    "uri": "http://edamontology.org/topic_2258"
                }
            ],
            "owner": "ELIXIR-CZ",
            "cost": "Free of charge",
            "download": [],
            "validated": 0,
            "publication": [
                {
                    "doi": "10.1186/s13321-018-0282-y",
                    "version": null,
                    "pmid": null,
                    "type": "Method",
                    "pmcid": null,
                    "metadata": {
                        "title": "Sachem: a chemical cartridge for high-performance substructure search",
                        "abstract": "© 2018, The Author(s).Background: Structure search is one of the valuable capabilities of small-molecule databases. Fingerprint-based screening methods are usually employed to enhance the search performance by reducing the number of calls to the verification procedure. In substructure search, fingerprints are designed to capture important structural aspects of the molecule to aid the decision about whether the molecule contains a given substructure. Currently available cartridges typically provide acceptable search performance for processing user queries, but do not scale satisfactorily with dataset size. Results: We present Sachem, a new open-source chemical cartridge that implements two substructure search methods: The first is a performance-oriented reimplementation of substructure indexing based on the OrChem fingerprint, and the second is a novel method that employs newly designed fingerprints stored in inverted indices. We assessed the performance of both methods on small, medium, and large datasets containing 1, 10, and 94 million compounds, respectively. Comparison of Sachem with other freely available cartridges revealed improvements in overall performance, scaling potential and screen-out efficiency. Conclusions: The Sachem cartridge allows efficient substructure searches in databases of all sizes. The sublinear performance scaling of the second method and the ability to efficiently query large amounts of pre-extracted information may together open the door to new applications for substructure searches.",
                        "citationCount": 0,
                        "authors": [
                            {
                                "name": "Kratochvil M."
                            },
                            {
                                "name": "Vondrasek J."
                            },
                            {
                                "name": "Galgonek J."
                            }
                        ],
                        "date": "2018-12-01T00:00:00Z",
                        "journal": "Journal of Cheminformatics"
                    }
                }
            ],
            "homepage_status": 0,
            "credit": [
                {
                    "typeRole": [
                        "Maintainer",
                        "Developer"
                    ],
                    "name": "Jakub Galgonek",
                    "url": null,
                    "note": null,
                    "orcidid": null,
                    "typeEntity": "Person",
                    "email": "jakub.galgonek@uochb.cas.cz"
                },
                {
                    "typeRole": [
                        "Maintainer"
                    ],
                    "name": "Mirek Kratochvíl",
                    "url": null,
                    "note": null,
                    "orcidid": null,
                    "typeEntity": "Person",
                    "email": null
                },
                {
                    "typeRole": [
                        "Provider"
                    ],
                    "name": "IOCB CAS",
                    "url": null,
                    "note": null,
                    "orcidid": null,
                    "typeEntity": "Institute",
                    "email": null
                }
            ],
            "biotoolsCURIE": "biotools:IDSM",
            "elixirPlatform": [
                "Data"
            ],
            "elixirNode": [
                "Czech Republic"
            ],
            "version": [],
            "elixir_badge": 0,
            "homepage": "https://idsm.elixir-czech.cz/",
            "function": [
                {
                    "note": null,
                    "input": [
                        {
                            "data": {
                                "term": "Small molecule structure",
                                "uri": "http://edamontology.org/data_1463"
                            },
                            "format": [
                                {
                                    "term": "Chemical formula format",
                                    "uri": "http://edamontology.org/format_2035"
                                }
                            ]
                        }
                    ],
                    "operation": [
                        {
                            "term": "Database search",
                            "uri": "http://edamontology.org/operation_2421"
                        }
                    ],
                    "cmd": null,
                    "output": [
                        {
                            "data": {
                                "term": "Small molecule report",
                                "uri": "http://edamontology.org/data_0962"
                            },
                            "format": [
                                {
                                    "term": "CSV",
                                    "uri": "http://edamontology.org/format_3752"
                                },
                                {
                                    "term": "HTML",
                                    "uri": "http://edamontology.org/format_2331"
                                }
                            ]
                        }
                    ]
                }
            ],
            "lastUpdate": "2019-04-15T21:50:41.657538Z",
            "otherID": [],
            "description": "Integrated Database of Small Molecules",
            "toolType": [
                "Database portal"
            ],
            "editPermission": {
                "type": "private",
                "authors": []
            },
            "language": [],
            "link": [],
            "biotoolsID": "IDSM",
            "additionDate": "2019-04-15T21:50:28Z",
            "name": "IDSM",
            "license": "Other",
            "documentation": [
                {
                    "url": "https://idsm.elixir-czech.cz/sparql/manual.html",
                    "note": null,
                    "type": "Manual"
                }
            ],
            "maturity": "Mature",
            "operatingSystem": []
        },
        {
            "collectionID": [],
            "accessibility": [
                "Open access"
            ],
            "topic": [
                {
                    "term": "Gene transcripts",
                    "uri": "http://edamontology.org/topic_3512"
                },
                {
                    "term": "RNA splicing",
                    "uri": "http://edamontology.org/topic_3320"
                },
                {
                    "term": "DNA structural variation",
                    "uri": "http://edamontology.org/topic_3175"
                }
            ],
            "owner": "suhrig",
            "cost": "Free of charge",
            "download": [
                {
                    "url": "https://github.com/suhrig/arriba/releases/",
                    "note": null,
                    "version": null,
                    "type": "Binary package"
                }
            ],
            "validated": 0,
            "publication": [],
            "homepage_status": 0,
            "credit": [],
            "biotoolsCURIE": "biotools:Arriba",
            "elixirPlatform": [],
            "elixirNode": [],
            "version": [],
            "elixir_badge": 0,
            "homepage": "https://github.com/suhrig/arriba/",
            "function": [
                {
                    "note": null,
                    "input": [
                        {
                            "data": {
                                "term": "RNA sequence",
                                "uri": "http://edamontology.org/data_3495"
                            },
                            "format": [
                                {
                                    "term": "BAM",
                                    "uri": "http://edamontology.org/format_2572"
                                },
                                {
                                    "term": "SAM",
                                    "uri": "http://edamontology.org/format_2573"
                                },
                                {
                                    "term": "CRAM",
                                    "uri": "http://edamontology.org/format_3462"
                                },
                                {
                                    "term": "FASTQ-illumina",
                                    "uri": "http://edamontology.org/format_1931"
                                }
                            ]
                        }
                    ],
                    "operation": [
                        {
                            "term": "Split read mapping",
                            "uri": "http://edamontology.org/operation_3199"
                        },
                        {
                            "term": "Structural variation detection",
                            "uri": "http://edamontology.org/operation_3228"
                        }
                    ],
                    "cmd": null,
                    "output": [
                        {
                            "data": {
                                "term": "Sequence variations",
                                "uri": "http://edamontology.org/data_3498"
                            },
                            "format": [
                                {
                                    "term": "TSV",
                                    "uri": "http://edamontology.org/format_3475"
                                }
                            ]
                        }
                    ]
                }
            ],
            "lastUpdate": "2019-04-07T15:56:34.398319Z",
            "otherID": [],
            "description": "Arriba is a command-line tool to detect gene fusions from RNA-Seq data based on the STAR aligner. In addition to fusions, it can detect exon duplications/inversions and truncations of genes (i.e., breakpoints in introns and intergenic regions). Arriba is the winner of the DREAM SMC-RNA Challenge.",
            "toolType": [
                "Command-line tool"
            ],
            "editPermission": {
                "type": "private",
                "authors": []
            },
            "language": [
                "C++"
            ],
            "link": [],
            "biotoolsID": "Arriba",
            "additionDate": "2019-02-08T22:48:19Z",
            "name": "Arriba",
            "license": "MIT",
            "documentation": [
                {
                    "url": "https://arriba.readthedocs.io/",
                    "note": null,
                    "type": "Manual"
                }
            ],
            "maturity": "Mature",
            "operatingSystem": [
                "Linux"
            ]
        },
        {
            "collectionID": [
                "Proteomics",
                "BioConductor"
            ],
            "accessibility": [],
            "topic": [
                {
                    "term": "Metabolomics",
                    "uri": "http://edamontology.org/topic_3172"
                },
                {
                    "term": "Proteomics experiment",
                    "uri": "http://edamontology.org/topic_3520"
                },
                {
                    "term": "Data visualisation",
                    "uri": "http://edamontology.org/topic_0092"
                }
            ],
            "owner": "bioconductor_import",
            "cost": null,
            "download": [
                {
                    "url": "http://bioconductor/packages/release/bioc/src/contrib/yamss_1.0.2.tar.gz",
                    "note": null,
                    "version": null,
                    "type": "Source code"
                }
            ],
            "validated": 0,
            "publication": [
                {
                    "doi": "10.1021/acs.analchem.6b04719",
                    "version": null,
                    "pmid": "28221771",
                    "type": "Primary",
                    "pmcid": "PMC5362739",
                    "metadata": null
                }
            ],
            "homepage_status": 0,
            "credit": [
                {
                    "typeRole": [
                        "Primary contact"
                    ],
                    "name": "Leslie Myint",
                    "url": null,
                    "note": null,
                    "orcidid": null,
                    "typeEntity": "Person",
                    "email": "lmyint1@jhu.edu"
                }
            ],
            "biotoolsCURIE": "biotools:yamss",
            "elixirPlatform": [],
            "elixirNode": [],
            "version": [
                "1.0.2"
            ],
            "elixir_badge": 0,
            "homepage": "http://bioconductor.org/packages/release/bioc/html/yamss.html",
            "function": [
                {
                    "note": null,
                    "input": [],
                    "operation": [
                        {
                            "term": "Spectral analysis",
                            "uri": "http://edamontology.org/operation_3214"
                        },
                        {
                            "term": "Mass spectrum visualisation",
                            "uri": "http://edamontology.org/operation_3694"
                        },
                        {
                            "term": "Metabolic network modelling",
                            "uri": "http://edamontology.org/operation_3660"
                        },
                        {
                            "term": "Statistical calculation",
                            "uri": "http://edamontology.org/operation_2238"
                        }
                    ],
                    "cmd": null,
                    "output": []
                }
            ],
            "lastUpdate": "2019-03-26T08:43:21Z",
            "otherID": [],
            "description": "Tools to analyze and visualize high-throughput metabolomics data aquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis.",
            "toolType": [
                "Command-line tool",
                "Library"
            ],
            "editPermission": {
                "type": "group",
                "authors": [
                    "ELIXIR-EE",
                    "proteomics.bio.tools"
                ]
            },
            "language": [
                "R"
            ],
            "link": [
                {
                    "url": "https://github.com/hansenlab/yamss",
                    "note": null,
                    "type": "Mirror"
                }
            ],
            "biotoolsID": "yamss",
            "additionDate": "2017-01-17T14:57:17Z",
            "name": "yamss",
            "license": "Artistic-2.0",
            "documentation": [
                {
                    "url": "http://bioconductor.org/packages/release/bioc/html/yamss.html",
                    "note": null,
                    "type": "Manual"
                }
            ],
            "maturity": null,
            "operatingSystem": [
                "Linux",
                "Windows",
                "Mac"
            ]
        },
        {
            "collectionID": [
                "ms-utils",
                "Proteomics"
            ],
            "accessibility": [],
            "topic": [
                {
                    "term": "Proteomics",
                    "uri": "http://edamontology.org/topic_0121"
                },
                {
                    "term": "Proteomics experiment",
                    "uri": "http://edamontology.org/topic_3520"
                }
            ],
            "owner": "msutils_import",
            "cost": null,
            "download": [],
            "validated": 0,
            "publication": [
                {
                    "doi": "10.1021/pr060154z",
                    "version": null,
                    "pmid": null,
                    "type": "Primary",
                    "pmcid": null,
                    "metadata": {
                        "title": "Protein cross-linking analysis using mass spectrometry, isotope-coded cross-linkers, and integrated computational data processing",
                        "abstract": "Distance constraints in proteins and protein complexes provide invaluable information for calculation of 3D structures, identification of protein binding partners and localization of protein-protein contact sites. We have developed an integrative approach to identify and characterize such sites through the analysis of proteolytic products derived from proteins chemically cross-linked by isotopically coded cross-linkers using LC-MALDI tandem mass spectrometry and computer software. This method is specifically tailored toward the rapid analysis of low microgram amounts of proteins or multimeric protein complexes cross-linked with nonlabeled and deuterium-labeled bis-NHS ester cross-linking reagents (both commercially available and readily synthesized). Through labeling with [18O]water solvent and LC-MALDI analysis, the method further allows the possible distinction between Type O and Type 1 or Type 2 modified peptides (monolinks and looplinks or cross-links), although such a distinction is more readily made from analysis of tandem mass spectrometry data. When applied to the bacterial Colicin E7 DNAse/lm7 heterodimeric protein complex, 23 cross-links were identified including six intersubunit cross-links, all between residues that are close in space when examined in the context of the X-ray structure of the heterodimer. In addition, cross-links were successfully identified in five single subunit proteins, beta-lactoglobulin, cytochrome c, lysozyme, myoglobin, and ribonuclease A, establishing the generality of the approach. © 2006 American Chemical Society.",
                        "citationCount": 84,
                        "authors": [
                            {
                                "name": "Seebacher J."
                            },
                            {
                                "name": "Mallick P."
                            },
                            {
                                "name": "Zhang N."
                            },
                            {
                                "name": "Eddes J.S."
                            },
                            {
                                "name": "Aebersold R."
                            },
                            {
                                "name": "Gelb M.H."
                            }
                        ],
                        "date": "2006-09-01T00:00:00Z",
                        "journal": "Journal of Proteome Research"
                    }
                }
            ],
            "homepage_status": 0,
            "credit": [
                {
                    "typeRole": [
                        "Documentor"
                    ],
                    "name": null,
                    "url": "http://ms-utils.org",
                    "note": null,
                    "orcidid": null,
                    "typeEntity": "Person",
                    "email": "webmaster@ms-utils.org"
                }
            ],
            "biotoolsCURIE": "biotools:xlink",
            "elixirPlatform": [],
            "elixirNode": [],
            "version": [],
            "elixir_badge": 0,
            "homepage": "http://tools.proteomecenter.org/XLink.php",
            "function": [
                {
                    "note": null,
                    "input": [],
                    "operation": [
                        {
                            "term": "Protein feature detection",
                            "uri": "http://edamontology.org/operation_3092"
                        },
                        {
                            "term": "Protein structure analysis",
                            "uri": "http://edamontology.org/operation_2406"
                        }
                    ],
                    "cmd": null,
                    "output": []
                }
            ],
            "lastUpdate": "2019-03-26T08:42:55Z",
            "otherID": [],
            "description": "Set of tools for analysis of data from crosslinked and digested protein complexes.",
            "toolType": [
                "Command-line tool"
            ],
            "editPermission": {
                "type": "group",
                "authors": [
                    "proteomics.bio.tools"
                ]
            },
            "language": [
                "Java",
                "Perl"
            ],
            "link": [
                {
                    "url": "http://ms-utils.org",
                    "note": null,
                    "type": "Registry"
                }
            ],
            "biotoolsID": "xlink",
            "additionDate": "2017-01-17T14:51:44Z",
            "name": "XLink",
            "license": null,
            "documentation": [
                {
                    "url": "http://tools.proteomecenter.org/software/xlink/XLINK_Software_Tools/XLINK_Software_Manual_0.93.html",
                    "note": null,
                    "type": "Manual"
                }
            ],
            "maturity": null,
            "operatingSystem": [
                "Linux",
                "Windows",
                "Mac"
            ]
        },
        {
            "collectionID": [
                "Proteomics",
                "Bioconductor"
            ],
            "accessibility": [],
            "topic": [
                {
                    "term": "Proteomics",
                    "uri": "http://edamontology.org/topic_0121"
                },
                {
                    "term": "Transcriptomics",
                    "uri": "http://edamontology.org/topic_3308"
                }
            ],
            "owner": "n.m.palmblad@lumc.nl",
            "cost": null,
            "download": [
                {
                    "url": "https://www.bioconductor.org/packages/release/bioc/html/XINA.html",
                    "note": null,
                    "version": "1.1.1",
                    "type": "Binary package"
                }
            ],
            "validated": 0,
            "publication": [
                {
                    "doi": "10.1021/acs.jproteome.8b00615",
                    "version": "1.1.1",
                    "pmid": "30370770",
                    "type": "Primary",
                    "pmcid": null,
                    "metadata": {
                        "title": "XINA: A Workflow for the Integration of Multiplexed Proteomics Kinetics Data with Network Analysis",
                        "abstract": "Copyright © 2018 American Chemical Society. Quantitative proteomics experiments, using for instance isobaric tandem mass tagging approaches, are conducive to measuring changes in protein abundance over multiple time points in response to one or more conditions or stimulations. The aim is often to determine which proteins exhibit similar patterns within and across experimental conditions, since proteins with coabundance patterns may have common molecular functions related to a given stimulation. In order to facilitate the identification and analyses of coabundance patterns within and across conditions, we previously developed a software inspired by the isobaric mass tagging method itself. Specifically, multiple data sets are tagged in silico and combined for subsequent subgrouping into multiple clusters within a single output depicting the variation across all conditions, converting a typical inter-data-set comparison into an intra-data-set comparison. An updated version of our software, XINA, not only extracts coabundance profiles within and across experiments but also incorporates protein-protein interaction databases and integrative resources such as KEGG to infer interactors and molecular functions, respectively, and produces intuitive graphical outputs. In this report, we compare the kinetics profiles of >5600 unique proteins derived from three macrophage cell culture experiments and demonstrate through intuitive visualizations that XINA identifies key regulators of macrophage activation via their coabundance patterns.",
                        "citationCount": 0,
                        "authors": [
                            {
                                "name": "Lee L.H."
                            },
                            {
                                "name": "Halu A."
                            },
                            {
                                "name": "Morgan S."
                            },
                            {
                                "name": "Iwata H."
                            },
                            {
                                "name": "Aikawa M."
                            },
                            {
                                "name": "Singh S.A."
                            }
                        ],
                        "date": "2019-02-01T00:00:00Z",
                        "journal": "Journal of Proteome Research"
                    }
                }
            ],
            "homepage_status": 0,
            "credit": [],
            "biotoolsCURIE": "biotools:xina",
            "elixirPlatform": [],
            "elixirNode": [],
            "version": [
                "1.1.1"
            ],
            "elixir_badge": 0,
            "homepage": "https://www.bioconductor.org/packages/devel/bioc/html/XINA.html",
            "function": [
                {
                    "note": null,
                    "input": [
                        {
                            "data": {
                                "term": "Expression data",
                                "uri": "http://edamontology.org/data_2603"
                            },
                            "format": [
                                {
                                    "term": "CSV",
                                    "uri": "http://edamontology.org/format_3752"
                                }
                            ]
                        }
                    ],
                    "operation": [
                        {
                            "term": "Pathway or network analysis",
                            "uri": "http://edamontology.org/operation_2497"
                        }
                    ],
                    "cmd": null,
                    "output": [
                        {
                            "data": {
                                "term": "Plot",
                                "uri": "http://edamontology.org/data_2884"
                            },
                            "format": [
                                {
                                    "term": "PDF",
                                    "uri": "http://edamontology.org/format_3508"
                                }
                            ]
                        }
                    ]
                }
            ],
            "lastUpdate": "2019-03-26T08:42:50Z",
            "otherID": [],
            "description": "An R package for network analyses from multiplexed, time-resolved proteomics or trascriptomics data",
            "toolType": [
                "Library"
            ],
            "editPermission": {
                "type": "group",
                "authors": [
                    "proteomics.bio.tools"
                ]
            },
            "language": [
                "R"
            ],
            "link": [
                {
                    "url": "https://www.bioconductor.org/packages/release/bioc/html/XINA.html",
                    "note": null,
                    "type": "Registry"
                }
            ],
            "biotoolsID": "xina",
            "additionDate": "2019-01-23T10:46:25Z",
            "name": "XINA",
            "license": "GPL-3.0",
            "documentation": [
                {
                    "url": "https://www.bioconductor.org/packages/devel/bioc/manuals/XINA/man/XINA.pdf",
                    "note": null,
                    "type": "Manual"
                }
            ],
            "maturity": null,
            "operatingSystem": [
                "Linux",
                "Windows",
                "Mac"
            ]
        },
        {
            "collectionID": [
                "Proteomics"
            ],
            "accessibility": [],
            "topic": [
                {
                    "term": "Proteomics",
                    "uri": "http://edamontology.org/topic_0121"
                },
                {
                    "term": "Proteomics experiment",
                    "uri": "http://edamontology.org/topic_3520"
                },
                {
                    "term": "Sequence analysis",
                    "uri": "http://edamontology.org/topic_0080"
                }
            ],
            "owner": "mbs_import",
            "cost": null,
            "download": [],
            "validated": 0,
            "publication": [
                {
                    "doi": null,
                    "version": null,
                    "pmid": "27479329",
                    "type": null,
                    "pmcid": null,
                    "metadata": {
                        "title": "TRIC: An automated alignment strategy for reproducible protein quantification in targeted proteomics",
                        "abstract": "© 2016 Nature America, Inc. All rights reserved. Next-generation mass spectrometric (MS) techniques such as SWATH-MS have substantially increased the throughput and reproducibility of proteomic analysis, but ensuring consistent quantification of thousands of peptide analytes across multiple liquid chromatography-tandem MS (LC-MS/MS) runs remains a challenging and laborious manual process. To produce highly consistent and quantitatively accurate proteomics data matrices in an automated fashion, we developed TRIC (http://proteomics.ethz.ch/tric/), a software tool that utilizes fragment-ion data to perform cross-run alignment, consistent peak-picking and quantification for high-throughput targeted proteomics. TRIC reduced the identification error compared to a state-of-the-art SWATH-MS analysis without alignment by more than threefold at constant recall while correcting for highly nonlinear chromatographic effects. On a pulsed-SILAC experiment performed on human induced pluripotent stem cells, TRIC was able to automatically align and quantify thousands of light and heavy isotopic peak groups. Thus, TRIC fills a gap in the pipeline for automated analysis of massively parallel targeted proteomics data sets.",
                        "citationCount": 31,
                        "authors": [
                            {
                                "name": "Rost H.L."
                            },
                            {
                                "name": "Liu Y."
                            },
                            {
                                "name": "D'Agostino G."
                            },
                            {
                                "name": "Zanella M."
                            },
                            {
                                "name": "Navarro P."
                            },
                            {
                                "name": "Rosenberger G."
                            },
                            {
                                "name": "Collins B.C."
                            },
                            {
                                "name": "Gillet L."
                            },
                            {
                                "name": "Testa G."
                            },
                            {
                                "name": "Malmstrom L."
                            },
                            {
                                "name": "Aebersold R."
                            }
                        ],
                        "date": "2016-08-30T00:00:00Z",
                        "journal": "Nature Methods"
                    }
                }
            ],
            "homepage_status": 0,
            "credit": [
                {
                    "typeRole": [
                        "Primary contact"
                    ],
                    "name": null,
                    "url": "http://www.imsb.ethz.ch/research/aebersold.html",
                    "note": null,
                    "orcidid": null,
                    "typeEntity": "Person",
                    "email": null
                },
                {
                    "typeRole": [
                        "Primary contact"
                    ],
                    "name": null,
                    "url": "https://github.com/msproteomicstools",
                    "note": null,
                    "orcidid": null,
                    "typeEntity": "Person",
                    "email": null
                }
            ],
            "biotoolsCURIE": "biotools:tric",
            "elixirPlatform": [],
            "elixirNode": [],
            "version": [],
            "elixir_badge": 0,
            "homepage": "http://proteomics.ethz.ch/tric/",
            "function": [
                {
                    "note": null,
                    "input": [],
                    "operation": [
                        {
                            "term": "Sequence alignment",
                            "uri": "http://edamontology.org/operation_0292"
                        }
                    ],
                    "cmd": null,
                    "output": []
                }
            ],
            "lastUpdate": "2019-03-26T08:41:37Z",
            "otherID": [],
            "description": "An alignment software for targeted proteomics (SRM or SWATH-MS) data. It uses a graph-based alignment strategy based on non-linear retention time correction to integrate information from all available runs. The input consists of a set of csv files derived from a targeted proteomics experiment generated by OpenSWATH (using either mProphet or pyProphet) or generated by Peakview.",
            "toolType": [
                "Command-line tool"
            ],
            "editPermission": {
                "type": "group",
                "authors": [
                    "proteomics.bio.tools"
                ]
            },
            "language": [
                "Python"
            ],
            "link": [
                {
                    "url": "http://www.mybiosoftware.com/tric-alignment-tool-for-targeted-proteomics.html",
                    "note": null,
                    "type": "Registry"
                }
            ],
            "biotoolsID": "tric",
            "additionDate": "2017-08-03T19:02:56Z",
            "name": "TRIC",
            "license": null,
            "documentation": [
                {
                    "url": "http://proteomics.ethz.ch/msproteomicstools/",
                    "note": null,
                    "type": "General"
                },
                {
                    "url": "https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md",
                    "note": null,
                    "type": "Manual"
                }
            ],
            "maturity": null,
            "operatingSystem": [
                "Linux"
            ]
        },
        {
            "collectionID": [
                "de.NBI",
                "Proteomics",
                "Bioconductor"
            ],
            "accessibility": [],
            "topic": [
                {
                    "term": "Drug discovery",
                    "uri": "http://edamontology.org/topic_3336"
                },
                {
                    "term": "Proteomics",
                    "uri": "http://edamontology.org/topic_0121"
                },
                {
                    "term": "Proteomics experiment",
                    "uri": "http://edamontology.org/topic_3520"
                }
            ],
            "owner": "hdhub",
            "cost": "Free of charge",
            "download": [],
            "validated": 0,
            "publication": [],
            "homepage_status": 0,
            "credit": [
                {
                    "typeRole": [
                        "Maintainer"
                    ],
                    "name": "Dorothee Childs",
                    "url": null,
                    "note": null,
                    "orcidid": null,
                    "typeEntity": "Person",
                    "email": null
                },
                {
                    "typeRole": [
                        "Developer"
                    ],
                    "name": "Nils Kurzawa",
                    "url": null,
                    "note": null,
                    "orcidid": null,
                    "typeEntity": "Person",
                    "email": null
                },
                {
                    "typeRole": [
                        "Primary contact"
                    ],
                    "name": "Dorothee Childs",
                    "url": null,
                    "note": null,
                    "orcidid": null,
                    "typeEntity": "Person",
                    "email": "dorothee.childs@embl.de"
                }
            ],
            "biotoolsCURIE": "biotools:tpp",
            "elixirPlatform": [],
            "elixirNode": [],
            "version": [
                "3.4.2"
            ],
            "elixir_badge": 0,
            "homepage": "https://bioconductor.org/packages/TPP/",
            "function": [
                {
                    "note": null,
                    "input": [],
                    "operation": [
                        {
                            "term": "Protein structure analysis",
                            "uri": "http://edamontology.org/operation_2406"
                        }
                    ],
                    "cmd": null,
                    "output": []
                }
            ],
            "lastUpdate": "2019-03-26T08:41:27Z",
            "otherID": [],
            "description": "Analyze thermal proteome profiling (TPP) experiments with varying temperatures (TR) or compound concentrations (CCR).",
            "toolType": [
                "Command-line tool"
            ],
            "editPermission": {
                "type": "group",
                "authors": [
                    "proteomics.bio.tools"
                ]
            },
            "language": [
                "R"
            ],
            "link": [],
            "biotoolsID": "tpp",
            "additionDate": "2017-06-23T07:16:50Z",
            "name": "TPP",
            "license": "Artistic-2.0",
            "documentation": [
                {
                    "url": "https://bioconductor.org/packages/release/bioc/vignettes/TPP/inst/doc/TPP_introduction_1D.pdf",
                    "note": null,
                    "type": "Manual"
                },
                {
                    "url": "https://bioconductor.org/packages/release/bioc/vignettes/TPP/inst/doc/TPP_introduction_2D.pdf",
                    "note": null,
                    "type": "Manual"
                },
                {
                    "url": "https://bioconductor.org/packages/release/bioc/vignettes/TPP/inst/doc/NPARC_analysis_of_TPP_TR_data.pdf",
                    "note": null,
                    "type": "Manual"
                }
            ],
            "maturity": "Mature",
            "operatingSystem": [
                "Linux",
                "Windows",
                "Mac"
            ]
        },
        {
            "collectionID": [
                "Proteomics"
            ],
            "accessibility": [],
            "topic": [
                {
                    "term": "Protein structure analysis",
                    "uri": "http://edamontology.org/topic_2814"
                },
                {
                    "term": "Proteins",
                    "uri": "http://edamontology.org/topic_0078"
                },
                {
                    "term": "Structure analysis",
                    "uri": "http://edamontology.org/topic_0081"
                },
                {
                    "term": "Structure prediction",
                    "uri": "http://edamontology.org/topic_0082"
                },
                {
                    "term": "Gene and protein families",
                    "uri": "http://edamontology.org/topic_0623"
                },
                {
                    "term": "Proteomics",
                    "uri": "http://edamontology.org/topic_0121"
                }
            ],
            "owner": "ELIXIR-EE",
            "cost": null,
            "download": [],
            "validated": 0,
            "publication": [
                {
                    "doi": null,
                    "version": null,
                    "pmid": "18174182",
                    "type": null,
                    "pmcid": null,
                    "metadata": {
                        "title": "A note on difficult structure alignment problems",
                        "abstract": "Summary: Progress in structural biology depends on several key technologies. In particular tools for alignment and superposition of protein structures are indispensable. Here we describe the use of the TopMatch web service, an effective computational tool for protein structure alignment, for the visualization of structural similarities, and for highlighting relationships found in protein classifications. We provide several instructive examples. © 2008 The Author(s).",
                        "citationCount": 99,
                        "authors": [
                            {
                                "name": "Sippl M.J."
                            },
                            {
                                "name": "Wiederstein M."
                            }
                        ],
                        "date": "2008-02-01T00:00:00Z",
                        "journal": "Bioinformatics"
                    }
                }
            ],
            "homepage_status": 0,
            "credit": [
                {
                    "typeRole": [
                        "Primary contact"
                    ],
                    "name": "TopMatch Support",
                    "url": null,
                    "note": null,
                    "orcidid": null,
                    "typeEntity": "Person",
                    "email": "topmatch@came.sbg.ac.at"
                }
            ],
            "biotoolsCURIE": "biotools:topmatch",
            "elixirPlatform": [],
            "elixirNode": [],
            "version": [],
            "elixir_badge": 0,
            "homepage": "http://topmatch.services.came.sbg.ac.at/",
            "function": [
                {
                    "note": null,
                    "input": [],
                    "operation": [
                        {
                            "term": "Protein secondary structure comparison",
                            "uri": "http://edamontology.org/operation_2488"
                        },
                        {
                            "term": "Global structure alignment",
                            "uri": "http://edamontology.org/operation_0510"
                        },
                        {
                            "term": "Structure analysis",
                            "uri": "http://edamontology.org/operation_2480"
                        },
                        {
                            "term": "Structure alignment",
                            "uri": "http://edamontology.org/operation_0295"
                        }
                    ],
                    "cmd": null,
                    "output": []
                }
            ],
            "lastUpdate": "2019-03-26T08:41:14Z",
            "otherID": [],
            "description": "Computational tools for the alignment and superposition of protein structures are essential instruments in structural biology. TopMatch-web provides an easy-to-use interface to a suite of techniques for protein structure alignments. Given a pair of protein structures, TopMatch calculates a list of alignments ordered by structural similarity. The corresponding superpositions can be explored in a 3D molecule viewer which highlights the structurally equivalent parts of the proteins.",
            "toolType": [
                "Web application"
            ],
            "editPermission": {
                "type": "group",
                "authors": [
                    "proteomics.bio.tools"
                ]
            },
            "language": [
                "Java"
            ],
            "link": [],
            "biotoolsID": "topmatch",
            "additionDate": "2017-05-02T10:01:22Z",
            "name": "TopMatch",
            "license": null,
            "documentation": [
                {
                    "url": "https://topmatch.services.came.sbg.ac.at/help/tm_help.html",
                    "note": null,
                    "type": "Manual"
                }
            ],
            "maturity": null,
            "operatingSystem": [
                "Linux",
                "Windows",
                "Mac"
            ]
        },
        {
            "collectionID": [
                "Proteomics",
                "BioConductor"
            ],
            "accessibility": [],
            "topic": [
                {
                    "term": "Proteomics",
                    "uri": "http://edamontology.org/topic_0121"
                },
                {
                    "term": "Proteomics experiment",
                    "uri": "http://edamontology.org/topic_3520"
                }
            ],
            "owner": "shadi.m",
            "cost": "Free of charge",
            "download": [
                {
                    "url": "http://bioconductor.org/packages/release/bioc/src/contrib/topdownr_1.2.0.tar.gz",
                    "note": null,
                    "version": null,
                    "type": "Source package"
                }
            ],
            "validated": 0,
            "publication": [],
            "homepage_status": 0,
            "credit": [
                {
                    "typeRole": [
                        "Primary contact"
                    ],
                    "name": "Sebastian Gibb",
                    "url": null,
                    "note": null,
                    "orcidid": null,
                    "typeEntity": "Person",
                    "email": "mail@sebastiangibb.de"
                }
            ],
            "biotoolsCURIE": "biotools:topdownr",
            "elixirPlatform": [],
            "elixirNode": [],
            "version": [
                "1.2.0"
            ],
            "elixir_badge": 0,
            "homepage": "http://bioconductor.org/packages/release/bioc/html/topdownr.html",
            "function": [
                {
                    "note": null,
                    "input": [],
                    "operation": [
                        {
                            "term": "Analysis",
                            "uri": "http://edamontology.org/operation_2945"
                        }
                    ],
                    "cmd": null,
                    "output": []
                }
            ],
            "lastUpdate": "2019-03-26T08:41:10Z",
            "otherID": [],
            "description": "This package allows automatic and systemic investigation of fragment conditions. It creates Thermo Orbitrap Fusion Lumos method files to test hundreds of fragmentation conditions. Additionally it provides functions to analyse and process the generated MS data and determine the best conditions to maximise overall fragment coverage.",
            "toolType": [
                "Library"
            ],
            "editPermission": {
                "type": "group",
                "authors": [
                    "proteomics.bio.tools"
                ]
            },
            "language": [
                "R"
            ],
            "link": [
                {
                    "url": "https://github.com/sgibb/topdownr/",
                    "note": null,
                    "type": "Mirror"
                },
                {
                    "url": "https://github.com/sgibb/topdownr/issues/",
                    "note": null,
                    "type": "Issue tracker"
                }
            ],
            "biotoolsID": "topdownr",
            "additionDate": "2018-07-27T11:32:34Z",
            "name": "topdownr",
            "license": "GPL-3.0",
            "documentation": [
                {
                    "url": "http://bioconductor.org/packages/release/bioc/manuals/topdownr/man/topdownr.pdf",
                    "note": null,
                    "type": "Manual"
                }
            ],
            "maturity": null,
            "operatingSystem": [
                "Linux",
                "Windows",
                "Mac"
            ]
        },
        {
            "collectionID": [
                "Proteomics"
            ],
            "accessibility": [],
            "topic": [
                {
                    "term": "Proteomics",
                    "uri": "http://edamontology.org/topic_0121"
                }
            ],
            "owner": "n.m.palmblad@lumc.nl",
            "cost": "Free of charge",
            "download": [
                {
                    "url": "https://github.com/CMRose3355/TomahaqCompanionProgram",
                    "note": null,
                    "version": "1.0.2",
                    "type": "Binary package"
                },
                {
                    "url": "https://github.com/CMRose3355/TomahaqCompanion",
                    "note": null,
                    "version": "1.0.2",
                    "type": "Source package"
                }
            ],
            "validated": 0,
            "publication": [
                {
                    "doi": "10.1021/acs.jproteome.8b00767",
                    "version": "1.0.2",
                    "pmid": "30501201",
                    "type": "Primary",
                    "pmcid": null,
                    "metadata": {
                        "title": "TomahaqCompanion: A Tool for the Creation and Analysis of Isobaric Label Based Multiplexed Targeted Assays",
                        "abstract": "Copyright © 2018 American Chemical Society. Triggered by Offset, Multiplexed, Accurate mass, High resolution, and Absolute Quantitation (TOMAHAQ) is a recently introduced targeted proteomics method that combines peptide and sample multiplexing. TOMAHAQ assays enable sensitive and accurate multiplexed quantification by implementing an intricate data collection scheme that comprises multiple MSn scans, mass inclusion lists, and data-driven filters. Consequently, manual creation of TOMAHAQ methods can be time-consuming and error prone, while the resulting TOMAHAQ data may not be compatible with common mass spectrometry analysis pipelines. To address these concerns we introduce TomahaqCompanion, an open-source desktop application that enables rapid creation of TOMAHAQ methods and analysis of TOMAHAQ data. Starting from a list of peptide sequences, a user can perform each step of TOMAHAQ assay development including (1) generation of priming run target list, (2) analysis of priming run data, (3) generation of TOMAHAQ method file, and (4) analysis and export of quantitative TOMAHAQ data. We demonstrate the flexibility of TomahaqCompanion by creating a variety of methods testing TOMAHAQ parameters (e.g., number of SPS notches, run length, etc.). Lastly, we analyze an interference sample comprising heavy yeast peptides, a standard human peptide mixture, TMT11-plex, and super heavy TMT (shTMT) isobaric labels to demonstrate ∼10-200 attomol limit of quantification within a complex background using TOMAHAQ.",
                        "citationCount": 0,
                        "authors": [
                            {
                                "name": "Rose C.M."
                            },
                            {
                                "name": "Erickson B.K."
                            },
                            {
                                "name": "Schweppe D.K."
                            },
                            {
                                "name": "Viner R."
                            },
                            {
                                "name": "Choi J."
                            },
                            {
                                "name": "Rogers J."
                            },
                            {
                                "name": "Bomgarden R."
                            },
                            {
                                "name": "Gygi S.P."
                            },
                            {
                                "name": "Kirkpatrick D.S."
                            }
                        ],
                        "date": "2019-02-01T00:00:00Z",
                        "journal": "Journal of Proteome Research"
                    }
                }
            ],
            "homepage_status": 0,
            "credit": [],
            "biotoolsCURIE": "biotools:tomahaqcompanion",
            "elixirPlatform": [],
            "elixirNode": [],
            "version": [
                "1.0.2"
            ],
            "elixir_badge": 0,
            "homepage": "https://github.com/CMRose3355/TomahaqCompanionProgram",
            "function": [
                {
                    "note": "TomahaqCompanion outputs isobaric label based multiplexed targeted assays in a form readable by the mass spectrometer control software.",
                    "input": [
                        {
                            "data": {
                                "term": "Protein sequence (raw)",
                                "uri": "http://edamontology.org/data_2974"
                            },
                            "format": [
                                {
                                    "term": "CSV",
                                    "uri": "http://edamontology.org/format_3752"
                                }
                            ]
                        },
                        {
                            "data": {
                                "term": "Mass spectrometry spectra",
                                "uri": "http://edamontology.org/data_0943"
                            },
                            "format": [
                                {
                                    "term": "Thermo RAW",
                                    "uri": "http://edamontology.org/format_3712"
                                }
                            ]
                        }
                    ],
                    "operation": [
                        {
                            "term": "Design",
                            "uri": "http://edamontology.org/operation_2430"
                        }
                    ],
                    "cmd": null,
                    "output": [
                        {
                            "data": {
                                "term": "Data",
                                "uri": "http://edamontology.org/data_0006"
                            },
                            "format": []
                        }
                    ]
                }
            ],
            "lastUpdate": "2019-03-26T08:41:08Z",
            "otherID": [],
            "description": "Desktop application that enables rapid creation of TOMAHAQ methods and analysis of TOMAHAQ data.",
            "toolType": [
                "Desktop application"
            ],
            "editPermission": {
                "type": "group",
                "authors": [
                    "proteomics.bio.tools"
                ]
            },
            "language": [
                "C#"
            ],
            "link": [],
            "biotoolsID": "tomahaqcompanion",
            "additionDate": "2019-01-23T11:26:01Z",
            "name": "TomahaqCompanion",
            "license": "GPL-3.0",
            "documentation": [
                {
                    "url": "https://github.com/CMRose3355/TomahaqCompanionProgram/tree/master/StarterKit",
                    "note": null,
                    "type": "Manual"
                }
            ],
            "maturity": null,
            "operatingSystem": [
                "Windows"
            ]
        }
    ],
    "next": "?page=2"
}