Research products (435)
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435 Research products

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Wellcome Trust

ClustalW2 Phylogeny (EBI)
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2015Publisher:bio.toolsFunded by:WT, EC | ASSEMBLE
WT ,
EC| ASSEMBLE
Authors: Higgins, Des; Dispatcher, Job;
Phylogenetic tree generation from an alignment using neighbor-joining or UPGMA.
bio.toolsarrow_drop_down
bio.tools
Software . 2015
Data sources: bio.tools
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bio.tools
Software . 2015
Data sources: bio.tools
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rjorton/DinucISG: V1 - incl analysis files
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2021Publisher:ZenodoFunded by:WT | Mitigating bat viruses: f..., UKRI | Viral Genomics and Bioinf...
WT| Mitigating bat viruses: from forecasting spillover to control at the source ,
UKRI| Viral Genomics and Bioinformatics
Authors: Richard Orton;
doi: 10.5281/zenodo.5035606 , 10.5281/zenodo.5035607
doi: 10.5281/zenodo.5035606 , 10.5281/zenodo.5035607
V1 of the code and V6 and V8 of the ISG_CG analysis files
ZENODOarrow_drop_down
ZENODO
Software . 2021
Data sources: Datacite
ZENODO
Software . 2021
Data sources: ZENODO
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ZENODOarrow_drop_down
ZENODO
Software . 2021
Data sources: Datacite
ZENODO
Software . 2021
Data sources: ZENODO
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predictive-clinical-neuroscience/PCNportal: PCNportal version 1.0
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2023Publisher:ZenodoFunded by:WT | BRAINCHART: Normative bra...
WT| BRAINCHART: Normative brain charting for predicting and stratifying psychosis
Authors: PBarkema;
doi: 10.5281/zenodo.7708366 , 10.5281/zenodo.7708367
doi: 10.5281/zenodo.7708366 , 10.5281/zenodo.7708367
Initial release of PCNportal
ZENODOarrow_drop_down
ZENODO
Software . 2023
License: https://www.gnu.org/licenses/old-licenses/gpl-2.0-standalone.html
Data sources: Datacite
ZENODO
Software . 2023
Data sources: ZENODO
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ZENODOarrow_drop_down
ZENODO
Software . 2023
License: https://www.gnu.org/licenses/old-licenses/gpl-2.0-standalone.html
Data sources: Datacite
ZENODO
Software . 2023
Data sources: ZENODO
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GMX_lipid17.ff: Gromacs Port of the amber LIPID17 force field
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 English Publisher:ZenodoFunded by:WT | Oxford - OXION
WT| Oxford - OXION
Authors: Zhiyi Wu; Philip Biggin;
doi: 10.5281/zenodo.3560968
doi: 10.5281/zenodo.3560968
This is a Gromacs port of the amber LIPID17 force field. To use this force field, the user can construct the lipid bilayer using Charmm-GUI and convert the atom names to the amber atom names using charmmlipid2amber.py. This port has also retained the modular feature of the LIPID17 force field, where the user can customise the head group or acryl chain and use pdb2gmx to construct the topology. The coordinate files for the amber lipids can also be obtained from the `gro` folder. The force field `lipid17.ff`, itp file `lipid17.itp` and a custom PI head group are all included in the attached compressed file. For the details of the generation and validation protocol, please consult the relevant Github page.
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ZENODO
Software . 2019
Data sources: ZENODO
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ZENODO
Software . 2019
Data sources: ZENODO
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UniProtKB
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2015Publisher:bio.toolsFunded by:WT, NIH | Linking Text Mining and D..., NIH | Gene Ontology Consortium +12 projects
WT ,
NIH| Linking Text Mining and Data Mining for Biomedical Knowledge Discovery ,
NIH| Gene Ontology Consortium ,
NSF| ABI Development: Integrative Bioinformatics for Knowledge Discovery of PTM Networks ,
EC| GEN2PHEN ,
EC| MICROME ,
NIH| UniProt: A centralized protein sequence and function resource ,
NIH| UniProt: A Centralized Protein Sequence and Function Resource ,
NIH| PRO: A Protein Ontology in OBO Foundry for Integration of Biomedical Knowledge ,
NIH| Bioinformatics Core ,
NIH| Gene Ontology Consortium ,
NIH| UniProt: A Centralized Protein Sequence and Function Resource ,
NIH| Linking Text Mining and Data Mining for Biomedical Knowledge Discovery ,
NIH| Delaware INBRE ,
NIH| PRO: A Protein Ontology in OBO Foundry for Scalable Integration of Biomedical Knowledge
Authors: Helpdesk, UniProt;
The central hub for the collection of functional information on proteins with accurate, consistent and rich annotation. It consists of: UniProtKB/Swiss-Prot (manually-annotated records and curator-evaluated computational analysis) and UniProtKB/TrEMBL (computationally analyzed records awaiting manual annotation).
bio.toolsarrow_drop_down
bio.tools
Software . 2015
License: CC-BY-ND-3.0
Data sources: bio.tools
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bio.tools
Software . 2015
License: CC-BY-ND-3.0
Data sources: bio.tools
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GraphWeb
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2015Publisher:bio.toolsFunded by:WT
WT
Authors: Tooming, Laur; Reimand, Jüri; Vilo, Jaak;
Public web server for graph-based analysis of biological networks that: analyses directed and undirected, weighted and unweighted heterogeneous networks of genes, proteins and microarray probesets for many eukaryotic genomes; integrates multiple diverse datasets into global networks; incorporates multispecies data; filters nodes and edges; detects gene modules from networks; interprets discovered modules.
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bio.tools
Software . 2015
License: Freeware
Data sources: bio.tools
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bio.tools
Software . 2015
License: Freeware
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PhenoMiner
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2018Publisher:bio.toolsFunded by:EC | PHENOMINER, WT, ARC | A framework for building ...
EC| PHENOMINER ,
WT ,
ARC| A framework for building dynamic knowledge bases in the biomedical domain
Authors: Collier, Nigel;
Database of phenotypes extracted from the scientific literature using text mining.
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bio.tools
Software . 2018
Data sources: bio.tools
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bio.tools
Software . 2018
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iRODS
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019Publisher:bio.toolsFunded by:WT
WT
Authors: Team, iRODS Consortium;
Integrated Rule-Oriented Data System (iRODS) is open source data management software for a cancer genome analysis workflow.
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bio.tools
Software . 2019
License: BSD-3-Clause
Data sources: bio.tools
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bio.tools
Software . 2019
License: BSD-3-Clause
Data sources: bio.tools
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GOexpress
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2017 R Publisher:BioconductorFunded by:WT, WT | Computational Infection B..., EC | MACROSYS +1 projects
WT ,
WT| Computational Infection Biology ,
EC| MACROSYS ,
Department of Agriculture, Food and the Marine, Ireland
Authors: Rue-Albrecht, Kevin;
doi: 10.18129/b9.bioc.goexpress
doi: 10.18129/b9.bioc.goexpress
This package contains methods to visualise the expression profile of genes from a microarray or RNA-seq experiment, and offers a supervised clustering approach to identify GO terms containing genes with expression levels that best classify two or more predefined groups of samples.
bio.toolsarrow_drop_down
bio.tools
Software . 2017
License: GPL-3.0
Data sources: bio.tools
https://doi.org/10.18129/b9.bi...
Software . 2017
Data sources: Datacite
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bio.tools
Software . 2017
License: GPL-3.0
Data sources: bio.tools
https://doi.org/10.18129/b9.bi...
Software . 2017
Data sources: Datacite
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Variant Effect Predictor (VEP)
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2017 Perl Publisher:bio.toolsFunded by:EC | QUANTOMICS, EC | GEN2PHEN, WT | Ensembl +2 projects
EC| QUANTOMICS ,
EC| GEN2PHEN ,
WT| Ensembl ,
WT| Wellcome Trust Sanger Institute - generic account for deposition of all core- funded research papers ,
EC| MedBioinformatics
Authors: Ensembl; Form, Contact;
Tool for predicting effects of variants for any genome in Ensembl or with genome annotation (via GFF). This includes vertebrates and also plants, fungi, protists, metazoa and bacteria. There is a web and a REST API version but the most powerful is the Perl script version. See McLaren et al., 2016, Genome Biology
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bio.tools
Software . 2017
License: Apache-2.0
Data sources: bio.tools
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bio.tools
Software . 2017
License: Apache-2.0
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435 Research products

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ClustalW2 Phylogeny (EBI)
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2015Publisher:bio.toolsFunded by:WT, EC | ASSEMBLE
WT ,
EC| ASSEMBLE
Authors: Higgins, Des; Dispatcher, Job;
Phylogenetic tree generation from an alignment using neighbor-joining or UPGMA.
bio.toolsarrow_drop_down
bio.tools
Software . 2015
Data sources: bio.tools
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bio.tools
Software . 2015
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rjorton/DinucISG: V1 - incl analysis files
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2021Publisher:ZenodoFunded by:WT | Mitigating bat viruses: f..., UKRI | Viral Genomics and Bioinf...
WT| Mitigating bat viruses: from forecasting spillover to control at the source ,
UKRI| Viral Genomics and Bioinformatics
Authors: Richard Orton;
doi: 10.5281/zenodo.5035606 , 10.5281/zenodo.5035607
doi: 10.5281/zenodo.5035606 , 10.5281/zenodo.5035607
V1 of the code and V6 and V8 of the ISG_CG analysis files
ZENODOarrow_drop_down
ZENODO
Software . 2021
Data sources: Datacite
ZENODO
Software . 2021
Data sources: ZENODO
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ZENODO
Software . 2021
Data sources: Datacite
ZENODO
Software . 2021
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predictive-clinical-neuroscience/PCNportal: PCNportal version 1.0
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2023Publisher:ZenodoFunded by:WT | BRAINCHART: Normative bra...
WT| BRAINCHART: Normative brain charting for predicting and stratifying psychosis
Authors: PBarkema;
doi: 10.5281/zenodo.7708366 , 10.5281/zenodo.7708367
doi: 10.5281/zenodo.7708366 , 10.5281/zenodo.7708367
Initial release of PCNportal
ZENODOarrow_drop_down
ZENODO
Software . 2023
License: https://www.gnu.org/licenses/old-licenses/gpl-2.0-standalone.html
Data sources: Datacite
ZENODO
Software . 2023
Data sources: ZENODO
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ZENODO
Software . 2023
License: https://www.gnu.org/licenses/old-licenses/gpl-2.0-standalone.html
Data sources: Datacite
ZENODO
Software . 2023
Data sources: ZENODO
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GMX_lipid17.ff: Gromacs Port of the amber LIPID17 force field
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 English Publisher:ZenodoFunded by:WT | Oxford - OXION
WT| Oxford - OXION
Authors: Zhiyi Wu; Philip Biggin;
doi: 10.5281/zenodo.3560968
doi: 10.5281/zenodo.3560968
This is a Gromacs port of the amber LIPID17 force field. To use this force field, the user can construct the lipid bilayer using Charmm-GUI and convert the atom names to the amber atom names using charmmlipid2amber.py. This port has also retained the modular feature of the LIPID17 force field, where the user can customise the head group or acryl chain and use pdb2gmx to construct the topology. The coordinate files for the amber lipids can also be obtained from the `gro` folder. The force field `lipid17.ff`, itp file `lipid17.itp` and a custom PI head group are all included in the attached compressed file. For the details of the generation and validation protocol, please consult the relevant Github page.
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UniProtKB
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2015Publisher:bio.toolsFunded by:WT, NIH | Linking Text Mining and D..., NIH | Gene Ontology Consortium +12 projects
WT ,
NIH| Linking Text Mining and Data Mining for Biomedical Knowledge Discovery ,
NIH| Gene Ontology Consortium ,
NSF| ABI Development: Integrative Bioinformatics for Knowledge Discovery of PTM Networks ,
EC| GEN2PHEN ,
EC| MICROME ,
NIH| UniProt: A centralized protein sequence and function resource ,
NIH| UniProt: A Centralized Protein Sequence and Function Resource ,
NIH| PRO: A Protein Ontology in OBO Foundry for Integration of Biomedical Knowledge ,
NIH| Bioinformatics Core ,
NIH| Gene Ontology Consortium ,
NIH| UniProt: A Centralized Protein Sequence and Function Resource ,
NIH| Linking Text Mining and Data Mining for Biomedical Knowledge Discovery ,
NIH| Delaware INBRE ,
NIH| PRO: A Protein Ontology in OBO Foundry for Scalable Integration of Biomedical Knowledge
Authors: Helpdesk, UniProt;
The central hub for the collection of functional information on proteins with accurate, consistent and rich annotation. It consists of: UniProtKB/Swiss-Prot (manually-annotated records and curator-evaluated computational analysis) and UniProtKB/TrEMBL (computationally analyzed records awaiting manual annotation).
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GraphWeb
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2015Publisher:bio.toolsFunded by:WT
WT
Authors: Tooming, Laur; Reimand, Jüri; Vilo, Jaak;
Public web server for graph-based analysis of biological networks that: analyses directed and undirected, weighted and unweighted heterogeneous networks of genes, proteins and microarray probesets for many eukaryotic genomes; integrates multiple diverse datasets into global networks; incorporates multispecies data; filters nodes and edges; detects gene modules from networks; interprets discovered modules.
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PhenoMiner
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2018Publisher:bio.toolsFunded by:EC | PHENOMINER, WT, ARC | A framework for building ...
EC| PHENOMINER ,
WT ,
ARC| A framework for building dynamic knowledge bases in the biomedical domain
Authors: Collier, Nigel;
Database of phenotypes extracted from the scientific literature using text mining.
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