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{ "count": 9082, "next": "?page=2", "previous": null, "list": [ { "name": "Pepkio Cell Seeding Density Calculator", "description": "Derives cells per well and suspension pipette volumes for standard 6-, 12-, 24-, 48-, 96-, and 384-well plates from a hemocytometer stock count, trypan blue viability, and target seeding confluency, with QC flags for low viability and impractical transfers. A browser calculator supports interactive planning with cell-line presets; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client transmits parameters and returns structured plate tables and shareable run identifiers.", "homepage": "https://www.pepkio.com/tools/well-plate-seeding-density-calculator", "biotoolsID": "pepkio-well-plate-seeding-density-calculator", "biotoolsCURIE": "biotools:pepkio-well-plate-seeding-density-calculator", "version": [ "0.1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" }, { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [], "output": [], "note": "Web calculator for bench seeding; Python library and CLI for API-backed automation of the same cell seeding engine.", "cmd": null } ], "toolType": [ "Command-line tool", "Library", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3047", "term": "Molecular biology" }, { "uri": "http://edamontology.org/topic_3361", "term": "Laboratory techniques" }, { "uri": "http://edamontology.org/topic_2229", "term": "Cell biology" } ], "operatingSystem": [], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/pepkio/pepkio-well-plate-seeding-density-calculator", "type": [ "Repository" ], "note": null }, { "url": "https://www.pepkio.com/tools/well-plate-seeding-density-calculator", "type": [ "Service" ], "note": null }, { "url": "https://pypi.org/project/pepkio-well-plate-seeding-density-calculator/", "type": [ "Other" ], "note": "Python client on PyPI." } ], "download": [], "documentation": [ { "url": "https://www.pepkio.com/tools/well-plate-seeding-density-calculator", "type": [ "General" ], "note": null }, { "url": "https://github.com/pepkio/pepkio-well-plate-seeding-density-calculator", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": "Pepkio", "email": null, "url": "https://www.pepkio.com/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": "Pepkio develops software tools and bioinformatics solutions for life science researchers, including laboratory calculators and analysis services." } ], "owner": "pepkio", "additionDate": "2026-06-07T04:02:15.529158Z", "lastUpdate": "2026-06-07T04:02:36.627996Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Pepkio Standard Curve Calculator", "description": "Processes 96-well plate absorbance data through blank subtraction, regression fitting, and dilution correction to report sample concentrations with QC flags for BCA, Bradford, and ELISA workflows. A browser calculator supports interactive grid entry with CSV and PDF export; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client transmits plate layout and absorbance values and returns model comparison, per-sample concentrations, and shareable run identifiers.", "homepage": "https://www.pepkio.com/tools/absorbance-curve-calculator", "biotoolsID": "pepkio-absorbance-curve-calculator", "biotoolsCURIE": "biotools:pepkio-absorbance-curve-calculator", "version": [ "0.1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" }, { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" }, { "uri": "http://edamontology.org/operation_3659", "term": "Regression analysis" } ], "input": [], "output": [], "note": "Web calculator for plate-based standard-curve fitting; Python library and CLI for API-backed automation of the same absorbance-curve engine.", "cmd": null } ], "toolType": [ "Web application", "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3047", "term": "Molecular biology" }, { "uri": "http://edamontology.org/topic_3361", "term": "Laboratory techniques" }, { "uri": "http://edamontology.org/topic_3292", "term": "Biochemistry" } ], "operatingSystem": [], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/pepkio/pepkio-absorbance-curve-calculator", "type": [ "Repository" ], "note": null }, { "url": "https://www.pepkio.com/tools/absorbance-curve-calculator", "type": [ "Service" ], "note": null } ], "download": [], "documentation": [ { "url": "https://www.pepkio.com/tools/absorbance-curve-calculator", "type": [ "General" ], "note": null }, { "url": "https://github.com/pepkio/pepkio-absorbance-curve-calculator", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": "Pepkio", "email": null, "url": "https://www.pepkio.com/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": "Pepkio develops software tools and bioinformatics solutions for life science researchers, including laboratory calculators and analysis services." } ], "owner": "pepkio", "additionDate": "2026-06-07T03:07:06.267031Z", "lastUpdate": "2026-06-07T03:07:30.306304Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Pepkio Tm Annealing Temperature Calculator", "description": "Estimates PCR primer melting temperatures and polymerase-specific annealing temperatures from sequence and buffer inputs, with per-pair QC for hairpins, dimers, and Tm balance. A browser calculator supports interactive single-pair and batch entry (up to 200 pairs) with method comparison and export; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic for the API client is hosted remotely; sequences are transmitted for programmatic runs while the web interface performs calculations in the browser.", "homepage": "https://www.pepkio.com/tools/tm-annealing-temperature-calculator", "biotoolsID": "pepkio-tm-annealing-temperature-calculator", "biotoolsCURIE": "biotools:pepkio-tm-annealing-temperature-calculator", "version": [ "0.1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" }, { "uri": "http://edamontology.org/operation_0455", "term": "Nucleic acid thermodynamic property calculation" } ], "input": [], "output": [], "note": "Web calculator for in-browser Tm/Ta planning; Python library and CLI for API-backed automation of the same primer thermodynamics engine.", "cmd": null } ], "toolType": [ "Web application", "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0632", "term": "Probes and primers" }, { "uri": "http://edamontology.org/topic_3047", "term": "Molecular biology" }, { "uri": "http://edamontology.org/topic_3361", "term": "Laboratory techniques" } ], "operatingSystem": [], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/pepkio/pepkio-tm-annealing-temperature-calculator", "type": [ "Repository" ], "note": null }, { "url": "https://www.pepkio.com/tools/tm-annealing-temperature-calculator", "type": [ "Service" ], "note": null }, { "url": "https://pypi.org/project/pepkio-tm-annealing-temperature-calculator/", "type": [ "Other" ], "note": "Python client on PyPI." } ], "download": [], "documentation": [ { "url": "https://www.pepkio.com/tools/tm-annealing-temperature-calculator", "type": [ "General" ], "note": null }, { "url": "https://github.com/pepkio/pepkio-tm-annealing-temperature-calculator", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": "Pepkio", "email": null, "url": "https://www.pepkio.com/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": "Pepkio develops software tools and bioinformatics solutions for life science researchers, including laboratory calculators and analysis services." } ], "owner": "pepkio", "additionDate": "2026-06-07T01:12:57.723685Z", "lastUpdate": "2026-06-07T01:12:57.725718Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Pepkio pH Buffer Recipe Calculator", "description": "Computes weighed laboratory buffer recipes from target pH, concentration, and volume, accounting for separate preparation and working temperatures when pKa shifts with temperature. Supports calculator mode from dry reagents and stock dilution mode, returning acid and base masses, ionic strength estimates, optional NaCl adjustment, gravimetric and titration routes, and stepwise protocols. A browser calculator supports interactive recipe entry with shareable links; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client transmits parameters and returns structured recipe tables, compatibility warnings, and shareable run identifiers.", "homepage": "https://www.pepkio.com/tools/ph-buffer-recipe-calculator", "biotoolsID": "pepkio-ph-buffer-recipe-calculator", "biotoolsCURIE": "biotools:pepkio-ph-buffer-recipe-calculator", "version": [ "0.1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" }, { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [], "output": [], "note": "Web calculator for bench buffer planning; Python library and CLI for API-backed automation of the same pH buffer recipe engine.", "cmd": null } ], "toolType": [ "Command-line tool", "Library", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3292", "term": "Biochemistry" }, { "uri": "http://edamontology.org/topic_3047", "term": "Molecular biology" }, { "uri": "http://edamontology.org/topic_3361", "term": "Laboratory techniques" } ], "operatingSystem": [], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/pepkio/pepkio-ph-buffer-recipe-calculator", "type": [ "Repository" ], "note": null }, { "url": "https://www.pepkio.com/tools/ph-buffer-recipe-calculator", "type": [ "Service" ], "note": null }, { "url": "https://pypi.org/project/pepkio-ph-buffer-recipe-calculator/", "type": [ "Other" ], "note": "Python client on PyPI." } ], "download": [], "documentation": [ { "url": "https://www.pepkio.com/tools/ph-buffer-recipe-calculator", "type": [ "General" ], "note": null }, { "url": "https://github.com/pepkio/pepkio-ph-buffer-recipe-calculator", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": "Pepkio", "email": null, "url": "https://www.pepkio.com/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": "Pepkio develops software tools and bioinformatics solutions for life science researchers, including laboratory calculators and analysis services." } ], "owner": "pepkio", "additionDate": "2026-06-07T00:51:25.740335Z", "lastUpdate": "2026-06-07T00:51:37.892323Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Pepkio PCR Master Mix Calculator", "description": "Plans PCR and qPCR master-mix reagent volumes from stock and final concentrations, reaction counts, and pipetting overage, with consolidated totals when several assays are prepared together. A browser calculator supports interactive recipe entry with printable bench sheets; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client transmits parameters and returns structured volume tables, dilution warnings, and shareable run identifiers.", "homepage": "https://www.pepkio.com/tools/pcr-master-mix-calculator", "biotoolsID": "pepkio-pcr-master-mix-calculator", "biotoolsCURIE": "biotools:pepkio-pcr-master-mix-calculator", "version": [ "0.1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" }, { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [], "output": [], "note": "Web calculator for bench planning; Python library and CLI for API-backed automation of the same PCR master-mix engine.", "cmd": null } ], "toolType": [ "Web application", "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3047", "term": "Molecular biology" }, { "uri": "http://edamontology.org/topic_3361", "term": "Laboratory techniques" } ], "operatingSystem": [], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/pepkio/pepkio-pcr-master-mix-calculator", "type": [ "Repository" ], "note": null }, { "url": "https://www.pepkio.com/tools/pcr-master-mix-calculator", "type": [ "Service" ], "note": null }, { "url": "https://pypi.org/project/pepkio-pcr-master-mix-calculator/", "type": [ "Other" ], "note": "Python client on PyPI." } ], "download": [], "documentation": [ { "url": "https://www.pepkio.com/tools/pcr-master-mix-calculator", "type": [ "General" ], "note": null }, { "url": "https://github.com/pepkio/pepkio-pcr-master-mix-calculator", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": "Pepkio", "email": null, "url": "https://www.pepkio.com/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": "Pepkio develops software tools and bioinformatics solutions for life science researchers, including laboratory calculators and analysis services." } ], "owner": "pepkio", "additionDate": "2026-06-06T10:17:59.613852Z", "lastUpdate": "2026-06-06T10:17:59.615902Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Pepkio Molarity Solution Calculator", "description": "Computes laboratory solution preparation parameters—powder mass to weigh, stock and diluent volumes for single dilutions, and multi-step serial concentration tables—with correction for hydrated salts and supplier purity. A browser calculator supports interactive prep planning with saved recipes and shareable links; a Python client and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client transmits parameters and returns structured protocol steps and shareable run identifiers.", "homepage": "https://www.pepkio.com/tools/molarity-solution-calculator", "biotoolsID": "pepkio-molarity-solution-calculator", "biotoolsCURIE": "biotools:pepkio-molarity-solution-calculator", "version": [ "0.1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" }, { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [], "output": [], "note": "Web calculator for powder, dilution, and serial modes; Python library and CLI for API-backed automation of the same solution-prep engine.", "cmd": null } ], "toolType": [ "Web application", "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3047", "term": "Molecular biology" }, { "uri": "http://edamontology.org/topic_3361", "term": "Laboratory techniques" }, { "uri": "http://edamontology.org/topic_3292", "term": "Biochemistry" } ], "operatingSystem": [], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/pepkio/pepkio-molarity-solution-calculator", "type": [ "Repository" ], "note": null }, { "url": "https://www.pepkio.com/tools/molarity-solution-calculator", "type": [ "Service" ], "note": null }, { "url": "https://pypi.org/project/pepkio-molarity-solution-calculator/", "type": [ "Other" ], "note": "Python client on PyPI." } ], "download": [], "documentation": [ { "url": "https://www.pepkio.com/tools/molarity-solution-calculator", "type": [ "General" ], "note": null }, { "url": "https://github.com/pepkio/pepkio-molarity-solution-calculator", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": "Pepkio", "email": null, "url": "https://www.pepkio.com/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": "Pepkio develops software tools and bioinformatics solutions for life science researchers, including laboratory calculators and analysis services." } ], "owner": "pepkio", "additionDate": "2026-06-06T09:54:43.514157Z", "lastUpdate": "2026-06-06T09:55:01.920855Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Pepkio Serial Dilution Planner", "description": "Plans geometric serial dilution series for molecular biology and biochemistry workflows, rounding transfer volumes to declared pipette ranges and optional 96- or 384-well plate layouts. A browser calculator supports interactive protocol design; a Python client and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client transmits parameters and returns structured step tables and shareable run identifiers.", "homepage": "https://www.pepkio.com/tools/serial-dilution-planner", "biotoolsID": "pepkio-serial-dilution-planner", "biotoolsCURIE": "biotools:pepkio-serial-dilution-planner", "version": [ "0.1.2" ], "otherID": [ { "value": "doi:10.5281/zenodo.20555991", "type": "doi", "version": "0.1.2" } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" }, { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [], "output": [], "note": "Web calculator for bench planning; Python library and CLI for API-backed automation of the same dilution engine.", "cmd": null } ], "toolType": [ "Command-line tool", "Library", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3047", "term": "Molecular biology" }, { "uri": "http://edamontology.org/topic_3361", "term": "Laboratory techniques" }, { "uri": "http://edamontology.org/topic_3292", "term": "Biochemistry" } ], "operatingSystem": [], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/pepkio/pepkio-serial-dilution-planner", "type": [ "Repository" ], "note": null }, { "url": "https://www.pepkio.com/tools/serial-dilution-planner", "type": [ "Service" ], "note": null }, { "url": "https://doi.org/10.5281/zenodo.20555991", "type": [ "Other" ], "note": "Archived client release on Zenodo." } ], "download": [], "documentation": [ { "url": "https://www.pepkio.com/tools/serial-dilution-planner", "type": [ "General" ], "note": null }, { "url": "https://github.com/pepkio/pepkio-serial-dilution-planner", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": "Pepkio", "email": null, "url": "https://www.pepkio.com/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": "Pepkio develops software tools and bioinformatics solutions for life science researchers, including laboratory calculators and analysis services." } ], "owner": "pepkio", "additionDate": "2026-06-05T11:49:37.977245Z", "lastUpdate": "2026-06-05T11:49:37.979211Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "EGA", "description": "European genome-phenome Archive (EGA) - service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects.", "homepage": "https://ega-archive.org/", "biotoolsID": "ega", "biotoolsCURIE": "biotools:ega", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" }, { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" }, { "uri": "http://edamontology.org/operation_3436", "term": "Aggregation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2383", "term": "EGA accession" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2531", "term": "Experiment report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web API", "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_0607", "term": "Laboratory information management" }, { "uri": "http://edamontology.org/topic_3263", "term": "Data security" }, { "uri": "http://edamontology.org/topic_3366", "term": "Data integration and warehousing" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": null, "collectionID": [ "RD-connect", "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Data" ], "elixirNode": [ "Spain" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://ega-archive.org/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1038/ng.3312", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The European Genome-phenome Archive of human data consented for biomedical research", "abstract": "© 2015 Nature America, Inc. All rights reserved.The European Genome-phenome Archive (EGA) is a permanent archive that promotes the distribution and sharing of genetic and phenotypic data consented for specific approved uses but not fully open, public distribution. The EGA follows strict protocols for information management, data storage, security and dissemination. Authorized access to the data is managed in partnership with the data-providing organizations. The EGA includes major reference data collections for human genetics research.", "date": "2015-01-01T00:00:00Z", "citationCount": 161, "authors": [ { "name": "Lappalainen I." }, { "name": "Almeida-King J." }, { "name": "Kumanduri V." }, { "name": "Senf A." }, { "name": "Spalding J.D." }, { "name": "Ur-Rehman S." }, { "name": "Saunders G." }, { "name": "Kandasamy J." }, { "name": "Caccamo M." }, { "name": "Leinonen R." }, { "name": "Vaughan B." }, { "name": "Laurent T." }, { "name": "Rowland F." }, { "name": "Marin-Garcia P." }, { "name": "Barker J." }, { "name": "Jokinen P." }, { "name": "Torres A.C." }, { "name": "De Argila J.R." }, { "name": "Llobet O.M." }, { "name": "Medina I." }, { "name": "Puy M.S." }, { "name": "Alberich M." }, { "name": "De La Torre S." }, { "name": "Navarro A." }, { "name": "Paschall J." }, { "name": "Flicek P." } ], "journal": "Nature Genetics" } } ], "credit": [ { "name": "EMBL-EBI Databases", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "helpdesk@ega-archive.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "EMBL-EBI_Databases", "additionDate": "2015-06-11T13:36:28Z", "lastUpdate": "2026-06-04T08:07:27.522383Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE", "amy_jean" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CalibraCurve", "description": "A highly useful and flexible tool for calibration of targeted MS‐based measurements. CalibraCurve enables an automated batch-mode determination of dynamic linear ranges and quantification limits for both targeted proteomics and similar assays. The software uses a variety of measures to assess the accuracy of the calibration and provides intuitive visualizations.", "homepage": "https://github.com/mpc-bioinformatics/CalibraCurve", "biotoolsID": "calibracurve", "biotoolsCURIE": "biotools:calibracurve", "version": [ "2.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2945", "term": "Analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2526", "term": "Text data" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3591", "term": "tiff" } ] }, { "data": { "uri": "http://edamontology.org/data_2526", "term": "Text data" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Workflow", "Script", "Desktop application", "Plug-in" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3678", "term": "Experimental design and studies" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "BSD-3-Clause", "collectionID": [ "BioInfra.Prot", "de.NBI", "CUBiMed.RUB" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Germany" ], "elixirCommunity": [ "Proteomics" ], "link": [ { "url": "https://github.com/mpc-bioinformatics/CalibraCurve", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/mpc-bioinformatics/CalibraCurve", "type": "Downloads page", "note": null, "version": "2.0" } ], "documentation": [ { "url": "https://github.com/mpc-bioinformatics/CalibraCurve", "type": [ "Installation instructions", "Citation instructions", "General", "User manual", "Training material", "Terms of use" ], "note": null } ], "publication": [ { "doi": "10.1002/pmic.201900143", "pmid": "32086983", "pmcid": null, "type": [ "Primary" ], "version": "2.0", "note": null, "metadata": { "title": "CalibraCurve: A Tool for Calibration of Targeted MS-Based Measurements", "abstract": "Targeted proteomics techniques allow accurate quantitative measurements of analytes in complex matrices with dynamic linear ranges that span up to 4–5 orders of magnitude. Hence, targeted methods are promising for the development of robust protein assays in several sensitive areas, for example, in health care. However, exploiting the full method potential requires reliable determination of the dynamic range along with related quantification limits for each analyte. Here, a software named CalibraCurve that enables an automated batch-mode determination of dynamic linear ranges and quantification limits for both targeted proteomics and similar assays is presented. The software uses a variety of measures to assess the accuracy of the calibration, namely precision and trueness. Two different kinds of customizable graphs are created (calibration curves and response factor plots). The accuracy measures and the graphs offer an intuitive, detailed, and reliable opportunity to assess the quality of the model fit. Thus, CalibraCurve is deemed a highly useful and flexible tool to facilitate the development and control of reliable SRM/MRM-MS-based proteomics assays.", "date": "2020-06-01T00:00:00Z", "citationCount": 4, "authors": [ { "name": "Kohl M." }, { "name": "Stepath M." }, { "name": "Bracht T." }, { "name": "Megger D.A." }, { "name": "Sitek B." }, { "name": "Marcus K." }, { "name": "Eisenacher M." } ], "journal": "Proteomics" } } ], "credit": [ { "name": "PD Dr. Martin Eisenacher", "email": "martin.eisenacher@rub.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider", "Primary contact" ], "note": "If contacting use \"SPARROW\" in subject line to avoid mail deluge." }, { "name": "de.NBI", "email": null, "url": "https://www.denbi.de/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider", "Maintainer", "Support" ], "note": "Service provision and maintenance funded by de.NBI." }, { "name": "Dr. Michael Kohl", "email": "michael.kohl@rub.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "BioInfra.Prot", "additionDate": "2020-06-05T08:52:25Z", "lastUpdate": "2026-06-04T08:07:22.002962Z", "editPermission": { "type": "group", "authors": [ "karin" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PrimerPickr", "description": "Primerpickr is an open-source tool for rt-PCr primer picking powered by the aggregation of public usage of rt-pcr primers from open source papers. 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HULAFE", "email": "eucaim_project@iislafe.es", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Aikaterini Vraka", "email": "aikaterini_vraka@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0001-5984-904X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Pedro-Miguel Martínez-Gironés", "email": "pedromiguel_martinez@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9506-9451", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Support" ], "note": null } ], "owner": "casopon", "additionDate": "2025-05-29T10:41:57.535794Z", "lastUpdate": "2026-05-27T15:21:17.961394Z", "editPermission": { "type": "group", "authors": [ "pedromiguel_martinez_HULAFE" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "2D Digital Mammography Harmonization (EUCAIM-SW-046_T-01-03-008)", "description": "This preprocessing tool is design for 2D digital mammograms in DICOM format. 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It applies preprocessing steps as skull stripping, intra-patient registration, z-score normalization, patching, among others. 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HULAFE", "email": "eucaim_project@iislafe.es", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Maria Beser-Robles", "email": "maria_beser@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-0072-5525", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Pedro-Miguel Martinez-Girones", "email": "pedromiguel_martinez@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9506-9451", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Support" ], "note": null }, { "name": "Adrian Galiana-Bordera", "email": "adrian_galiana@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8324-8284", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Carina Soler-Pons", "email": "carina_soler@iislafe.es", "url": null, "orcidid": "https://orcid.org/0009-0000-2991-1391", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null }, { "name": "Leonor Cerda-Alberich", "email": "leonor_cerda@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-5567-4278", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider" ], "note": null }, { "name": "Luis Marti-Bonmati", "email": "luis_marti@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8234-010X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider" ], "note": null } ], "owner": "casopon", "additionDate": "2025-05-29T12:09:16.704255Z", "lastUpdate": "2026-05-27T15:20:39.690457Z", "editPermission": { "type": "group", "authors": [ "pedromiguel_martinez_HULAFE" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MR-based DIPG tumour detection and segmentation (EUCAIM-SW-020_T-01-02-003)", "description": "The tool performs an automatic segmentation of the possible DIPG tumours on MR images. 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The tool includes a complete workflow from DICOM images to DICOM seg tumoral masks.", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_dipg_tumour_detection_and_segmentation/info-tab", "biotoolsID": "mr-based_dipg_tumour_detection_and_segmentation", "biotoolsCURIE": "biotools:mr-based_dipg_tumour_detection_and_segmentation", "version": [ "2.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" } ] } ], "note": null, "cmd": "docker run --rm --gpus all \\\n -v /path/to/input:/input \\\n -v /path/to/output:/output \\\nharbor.eucaim.cancerimage.eu/processing-tools/mr-based_glioblastoma_tumour_detection_and_segmentation:latest \\\n --series-selector /input/config/series.csv" }, { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" } ] } ], "note": null, "cmd": "docker run --rm --gpus all \\\n -v /path/to/input:/input -v /path/to/output:/output harbor.eucaim.cancerimage.eu/processing-tools/mr-based_dipg_tumour_detection_and_segmentation:latest \\\n --json-args '{\"dataset_id\":\"DS1\",\"patient_id\":\"P1\",\"study_id\":\"S1\",\"sequences\":{\"T1w\":\"/input/DICOM/DS1/P1/S1/T1\",\"FLAIR\":\"/input/DICOM/DS1/P1/S1/FLAIR\"}}'" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_3365", "term": "Data architecture, analysis and design" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_dipg_tumour_detection_and_segmentation/info-tab", "type": [ "Software catalogue" ], "note": null }, { "url": "https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/", "type": [ "Social media" ], "note": null } ], "download": [], "documentation": [ { "url": "https://link.springer.com/article/10.1007/s10278-025-01557-9", "type": [ "General" ], "note": null }, { "url": "https://drive.eucaim.cancerimage.eu/s/5CL2H8tyMDzFHex", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.youtube.com/watch?v=f3DPS56z6oI&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=36", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.1007/s10278-025-01557-9", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "GIBI230 - HULAFE", "email": "eucaim_project@iislafe.es", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Matias Fernandez-Paton", "email": "matias_fernandez@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0001-9374-1411", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Pedro-Miguel Martinez-Girones", "email": "pedromiguel_martinez@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9506-9451", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor", "Support" ], "note": null }, { "name": "Adrian Galiana-Bordera", "email": "adrian_galiana@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8324-8284", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Carina Soler-Pons", "email": "carina_soler@iislafe.es", "url": null, "orcidid": "https://orcid.org/0009-0000-2991-1391", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Documentor", "Support" ], "note": null }, { "name": "Leonor Cerda-Alberich", "email": "leonor_cerda@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-5567-4278", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider" ], "note": null }, { "name": "Luis Marti-Bonmati", "email": "luis_marti@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8234-010X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider" ], "note": null } ], "owner": "casopon", "additionDate": "2025-05-29T09:19:51.404419Z", "lastUpdate": "2026-05-27T15:20:21.739269Z", "editPermission": { "type": "group", "authors": [ "pedromiguel_martinez_HULAFE" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MR-based neuroblastoma tumour detection and segmentation (EUCAIM-SW-019_T-01-02-002)", "description": "This tool is specifically designed and validated for automated detection and segmentation of neuroblastic tumours in T2-weighted magnetic resonance images (T2-MR) using deep learning. It processes DICOM or NIfTI input data and outputs in NIFTI or DICOM SEG.\n\nTRAINING & VALIDATION COHORTS:\n\nInitial Development (Veiga-Canuto 2022):\n-Training: 106 patients, 5-fold CV (median DSC 0.965 ± 0.018).\n-Internal validation: 26 patients (median DSC 0.918 ± 0.067).\n-Sources: La Fe (Spain), SIOPEN HR-NBL1/LINES, St. Anna (Austria), Pisa (Italy).\n-Mean age: 37.6 ± 39.3 months.\n-Median tumor volume: 116,518 mm³.\n\nExternal Validation (Veiga-Canuto 2023):\n-300 patients, 535 independent T2 MRI scans (486 at diagnosis, 49 post-chemotherapy).\n-Performance: median DSC 0.997 (0.944–1.000), 94% successful detection.\n-Sources: 12 European countries (HR-NBL1/SIOPEN 119, LINES/SIOPEN 107, German Registry 62, others 12).\n-Heterogeneous data: 1.5T (435), 3T (100); Siemens (318), Philips (109), GE (105), Canon (3).", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr_based_neuroblastoma_tumour_detection_and_segmentation/info-tab", "biotoolsID": "mr-based_neuroblastoma_tumour_detection_and_segmentation", "biotoolsCURIE": "biotools:mr-based_neuroblastoma_tumour_detection_and_segmentation", "version": [ "2.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" } ] } ], "note": null, "cmd": "docker run --rm \\\n -v \"<input_path>:/input\" \\\n -v \"<output_path>:/output\" \\\n --gpus all \\\n harbor.eucaim.cancerimage.eu/processing-tools/mr_based_neuroblastoma_tumour_detection_and_segmentation:2.0.0 \\\n --mode dicom-seg \\\n --series-selector /output/config/series_to_segment.csv \\\n --seg-series-number 2302001 \\\n --seg-algorithm-name \"nnUNet_Neuroblastoma_Primage_training\" \\\n --seg-coordinating-center \"EUCAIM Consortium\" \\\n --keep-nifti false" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_3365", "term": "Data architecture, analysis and design" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr_based_neuroblastoma_tumour_detection_and_segmentation/info-tab", "type": [ "Software catalogue" ], "note": null }, { "url": "https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/", "type": [ "Social media" ], "note": null } ], "download": [], "documentation": [ { "url": "https://drive.eucaim.cancerimage.eu/s/tS2W8nb38Zs2ZzK", "type": [ "User manual" ], "note": null }, { "url": "https://www.mdpi.com/2072-6694/14/15/3648", "type": [ "General" ], "note": null }, { "url": "https://drive.eucaim.cancerimage.eu/s/44BxMSNpxwgsZiE", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.youtube.com/watch?v=c7XOEGRA9aQ&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=12", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.3390/cancers14153648", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null }, { "doi": "10.3390/cancers15051622", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "GIBI230 - 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