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{ "count": 31839, "next": "?page=2", "previous": null, "list": [ { "name": "RINet", "description": "RINet is a bioinformatics tool for residue prioritization from protein structures. 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The accurate quantification of gene expression in specific conditions is important for functional assessment and requires an accurate PCR primer pair design to target all expressed alternative transcripts, a complex and prone-to-error task if performed manually. To efficiently address this task, we developed a pipeline, called IsoPrimer, to design PCR primer pairs targeting the specific set of expressed splicing variants of the genes of interest, to be used in quantitative PCR, e.g. in RNA-seq validation experiments. IsoPrimer, according to the level of expression of the splicing variants derived from an RNA-seq dataset, can: (i) identify the most expressed gene isoforms; (ii) design primer pairs overlapping exon-exon junctions common to the expressed variants; (iii) verify the specificity of the designed primer pairs.", "homepage": "https://github.com/BioinfoUNIBA/IsoPrimer", "biotoolsID": "IsoPrimer", "biotoolsCURIE": "biotools:IsoPrimer", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_4019", "term": "Biosciences" } ], "operatingSystem": [], "language": [], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Italy" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/BioinfoUNIBA/IsoPrimer", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/bioadv/vbaf171", "pmid": "40746506", "pmcid": "PMC12311343", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "ermes", "additionDate": "2026-01-30T16:39:34.710429Z", "lastUpdate": "2026-01-30T16:39:34.712643Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Cloud-based Workflow Manager (CloWM)", "description": "Data analysis in the life sciences often suffers from reproducibility, standardization and accessibility issues and these problems become even more severe with the escalating volume and complexity of data. While best-practice data analysis workflows try to tackle these challenges, many existing workflows still grapple with scalability issues, limited portability due to tight coupling with the execution environment and accessibility constraints arising from the absence of user-friendly interfaces. To overcome these issues, we created CloWM, a comprehensive cloud-based workflow management platform that allows the generic transformation of command-line driven workflows into user-friendly web-based services. CloWM offers the seamless integration of (1) scientific workflows written in the Nextflow DSL, (2) robust data storage, (3) a highly scalable compute layer for data-intensive analysis tasks and (4) a user-friendly interface.", "homepage": "https://clowm.bi.denbi.de", "biotoolsID": "clowm", "biotoolsCURIE": "biotools:clowm", "version": [], "otherID": [], "relation": [ { "biotoolsID": "sans", "type": "includes" } ], "function": [], "toolType": [ "Web service", "Bioinformatics portal", "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [], "language": [ "Python", "JavaScript" ], "license": "Apache-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [ { "url": "https://gitlab.ub.uni-bielefeld.de/cmg/clowm", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://clowm.bi.denbi.de/api/v1/openapi.json", "type": "API specification", "note": null, "version": null }, { "url": "https://gitlab.ub.uni-bielefeld.de/cmg/clowm", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://clowm.bi.denbi.de/api/v1/docs", "type": [ "API documentation" ], "note": null }, { "url": "https://clowm.bi.denbi.de/terms", "type": [ "Terms of use" ], "note": null }, { "url": "https://wiki.clowm.de", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.5281/zenodo.14039069", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Daniel Göbel", "email": "dgoebel@techfak.uni-bielefeld.de", "url": "https://ekvv.uni-bielefeld.de/pers_publ/publ/PersonDetail.jsp?personId=223066601", "orcidid": "https://orcid.org/0009-0009-9985-3823", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer", "Developer", "Primary contact" ], "note": null }, { "name": "Michael Beckstette", "email": "mbeckste@cebitec.uni-bielefeld.de", "url": null, "orcidid": "https://orcid.org/0000-0002-3707-1692", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Documentor" ], "note": null }, { "name": "Xaver Stiensmeier", "email": "xaver.stiensmeier@uni-bielefeld.de", "url": "https://ekvv.uni-bielefeld.de/pers_publ/publ/PersonDetail.jsp?personId=386908541", "orcidid": "https://orcid.org/0009-0005-3274-122X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "Bielefeld University", "email": null, "url": "https://www.uni-bielefeld.de", "orcidid": null, "gridid": null, "rorid": "02hpadn98", "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Genome Informatics", "email": null, "url": "https://gi.cebitec.uni-bielefeld.de", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "NFDI4Microbiota", "email": null, "url": "https://nfdi4microbiota.de", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [], "note": null } ], "owner": "dgoebel", "additionDate": "2025-04-09T13:19:17.715967Z", "lastUpdate": "2026-01-30T13:23:10.333194Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Stress Mouse Portal", "description": "Stressful experiences can induce maladaptive brain responses through gene expression changes, contributing to disorders such as depression and anxiety. We re-analysed 18 public mouse brain RNA-seq datasets from SRA using a unified computational workflow to ensure comparability. 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The service operates on a continuous open-call basis, with approved projects receiving a 1-year allocation that includes 50,000 CPU hours and 1 TB of storage by default, with the possibility to request additional resources. Proposals are evaluated by a scientific committee, with feedback typically provided within seven working days.\n\nFrom 2025, a pilot program enables the analysis of GDPR-protected sensitive data for up to two projects per year (maximum one per user or institution, first-come first-served). Projects involving non-sensitive data are unlimited and may be submitted at any time.", "homepage": "https://docs.google.com/forms/d/e/1FAIpQLSchmLCugIShXAneQmTgbM5SlPLDdZH0KCIECk0R9Tm6GTDcNw/viewform", "biotoolsID": "cineca-hpc", "biotoolsCURIE": "biotools:cineca-hpc", "version": [ "5" ], "otherID": [], "relation": [ { "biotoolsID": "kraken2", "type": "uses" }, { "biotoolsID": "annovar", "type": "uses" }, { "biotoolsID": "tophat2", "type": "uses" }, { "biotoolsID": "bowtie", "type": "uses" }, { "biotoolsID": "bowtie2", "type": "uses" }, { "biotoolsID": "hisat2", "type": "uses" }, { "biotoolsID": "vep", "type": "uses" }, { "biotoolsID": "gatk", "type": "uses" }, { "biotoolsID": "snakemake", "type": "uses" }, { "biotoolsID": "samtools", "type": "uses" }, { "biotoolsID": "R", "type": "uses" }, { "biotoolsID": "biopython", "type": "uses" }, { "biotoolsID": "hpc-reditools", "type": "uses" }, { "biotoolsID": "reditools", "type": "uses" }, { "biotoolsID": "tabix", "type": "uses" }, { 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The platform helps researchers stay up to date with the large volume of publications in their field by offering structured overviews that link directly to primary literature. The summaries are designed to support literature discovery and orientation, not to replace the underlying research papers. The platform includes topic-specific pages covering areas such as bioinformatics and computational biology.", "homepage": "https://summarized.science/", "biotoolsID": "summarized.science", "biotoolsCURIE": "biotools:summarized.science", "version": [ "1.1" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_4019", "term": "Biosciences" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://summarized.science/#newsletter", "type": [ "Mailing list" ], "note": "GDPR complient newsletter" } ], "download": [], "documentation": [ { "url": "https://summarized.science/about", "type": [ "Other" ], "note": "About page for the project" }, { "url": "https://summarized.science/faq", "type": [ "FAQ" ], "note": "FAQ page for the project" } ], "publication": [], "credit": [ { "name": "Niek Maas", "email": "hello@summarized.science", "url": "https://summarized.science/contact", "orcidid": "https://orcid.org/0000-0002-8745-4405", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "sybren", "additionDate": "2026-01-15T17:20:26.339869Z", "lastUpdate": "2026-01-15T17:25:05.336276Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MACSE", "description": "Aligning Protein-Coding Nucleotide Sequences with MACSE.\n\nMACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons.\n\nA wide range of molecular analyses relies on multiple sequence alignments (MSA).\n\nMACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and or stop codons.", "homepage": "https://bioweb.supagro.inra.fr/macse/", "biotoolsID": "macse", "biotoolsCURIE": "biotools:macse", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0492", "term": "Multiple sequence alignment" }, { "uri": "http://edamontology.org/operation_0496", "term": "Global alignment" }, { "uri": "http://edamontology.org/operation_0495", "term": "Local alignment" }, { "uri": "http://edamontology.org/operation_0265", "term": "Frameshift detection" }, { "uri": "http://edamontology.org/operation_3192", "term": "Sequence trimming" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0194", "term": "Phylogenomics" }, { "uri": "http://edamontology.org/topic_0081", "term": "Structure analysis" }, { "uri": "http://edamontology.org/topic_3945", "term": "Molecular evolution" }, { "uri": "http://edamontology.org/topic_3512", "term": "Gene transcripts" }, { "uri": "http://edamontology.org/topic_0108", "term": "Protein expression" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/ranwez/MACSE_V2_PIPELINES", "type": "Source code", "note": "Pipelines source code", "version": null } ], "documentation": [], "publication": [ { "doi": "10.1007/978-1-0716-1036-7_4", "pmid": "33289886", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Aligning Protein-Coding Nucleotide Sequences with MACSE", "abstract": "© 2021, Springer Science+Business Media, LLC, part of Springer Nature.Most genomic and evolutionary comparative analyses rely on accurate multiple sequence alignments. With their underlying codon structure, protein-coding nucleotide sequences pose a specific challenge for multiple sequence alignment. Multiple Alignment of Coding Sequences (MACSE) is a multiple sequence alignment program that provided the first automatic solution for aligning protein-coding gene datasets containing both functional and nonfunctional sequences (pseudogenes). Through its unique features, reliable codon alignments can be built in the presence of frameshifts and stop codons suitable for subsequent analysis of selection based on the ratio of nonsynonymous to synonymous substitutions. Here we offer a practical overview and guidelines on the use of MACSE v2. This major update of the initial algorithm now comes with a graphical interface providing user-friendly access to different subprograms to handle multiple alignments of protein-coding sequences. We also present new pipelines based on MACSE v2 subprograms to handle large datasets and distributed as Singularity containers. 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