1
|
Salazar GA, Luciani A, Watkins X, Kandasaamy S, Rice DL, Blum M, Bateman A, Martin M. Nightingale: web components for protein feature visualization. BIOINFORMATICS ADVANCES 2023; 3:vbad064. [PMID: 37359723 PMCID: PMC10287899 DOI: 10.1093/bioadv/vbad064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/20/2023] [Accepted: 05/23/2023] [Indexed: 06/28/2023]
Abstract
Motivation The visualization of biological data is a fundamental technique that enables researchers to understand and explain biology. Some of these visualizations have become iconic, for instance: tree views for taxonomy, cartoon rendering of 3D protein structures or tracks to represent features in a gene or protein, for instance in a genome browser. Nightingale provides visualizations in the context of proteins and protein features. Results Nightingale is a library of re-usable data visualization web components that are currently used by UniProt and InterPro, among other projects. The components can be used to display protein sequence features, variants, interaction data, 3D structure, etc. These components are flexible, allowing users to easily view multiple data sources within the same context, as well as compose these components to create a customized view. Availability and implementation Nightingale examples and documentation are freely available at https://ebi-webcomponents.github.io/nightingale/. It is distributed under the MIT license, and its source code can be found at https://github.com/ebi-webcomponents/nightingale.
Collapse
Affiliation(s)
- Gustavo A Salazar
- Macromolecules, Structure, Chemistry and Bioimaging Section, European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Aurélien Luciani
- Macromolecules, Structure, Chemistry and Bioimaging Section, European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Xavier Watkins
- Macromolecules, Structure, Chemistry and Bioimaging Section, European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Swaathi Kandasaamy
- Macromolecules, Structure, Chemistry and Bioimaging Section, European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Daniel L Rice
- Macromolecules, Structure, Chemistry and Bioimaging Section, European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Matthias Blum
- Macromolecules, Structure, Chemistry and Bioimaging Section, European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Alex Bateman
- Macromolecules, Structure, Chemistry and Bioimaging Section, European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Maria Martin
- Macromolecules, Structure, Chemistry and Bioimaging Section, European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| |
Collapse
|
2
|
Cai P, Liu S, Zhang D, Xing H, Han M, Liu D, Gong L, Hu QN. SynBioTools: a one-stop facility for searching and selecting synthetic biology tools. BMC Bioinformatics 2023; 24:152. [PMID: 37069545 PMCID: PMC10111727 DOI: 10.1186/s12859-023-05281-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/11/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND The rapid development of synthetic biology relies heavily on the use of databases and computational tools, which are also developing rapidly. While many tool registries have been created to facilitate tool retrieval, sharing, and reuse, no relatively comprehensive tool registry or catalog addresses all aspects of synthetic biology. RESULTS We constructed SynBioTools, a comprehensive collection of synthetic biology databases, computational tools, and experimental methods, as a one-stop facility for searching and selecting synthetic biology tools. SynBioTools includes databases, computational tools, and methods extracted from reviews via SCIentific Table Extraction, a scientific table-extraction tool that we built. Approximately 57% of the resources that we located and included in SynBioTools are not mentioned in bio.tools, the dominant tool registry. To improve users' understanding of the tools and to enable them to make better choices, the tools are grouped into nine modules (each with subdivisions) based on their potential biosynthetic applications. Detailed comparisons of similar tools in every classification are included. The URLs, descriptions, source references, and the number of citations of the tools are also integrated into the system. CONCLUSIONS SynBioTools is freely available at https://synbiotools.lifesynther.com/ . It provides end-users and developers with a useful resource of categorized synthetic biology databases, tools, and methods to facilitate tool retrieval and selection.
Collapse
Affiliation(s)
- Pengli Cai
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Sheng Liu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Dachuan Zhang
- Ecological Systems Design, Institute of Environmental Engineering, ETH Zurich, 8093, Zurich, Switzerland
| | - Huadong Xing
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Mengying Han
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Dongliang Liu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Linlin Gong
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Qian-Nan Hu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| |
Collapse
|
3
|
Ajadi MB, Soremekun OS, Adewumi AT, Kumalo HM, Soliman MES. Functional Analysis of Single Nucleotide Polymorphism in ZUFSP Protein and Implication in Pathogenesis. Protein J 2021; 40:28-40. [PMID: 33512633 DOI: 10.1007/s10930-021-09962-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2021] [Indexed: 11/25/2022]
Abstract
Researches have revealed that functional non-synonymous Single Nucleotide Polymorphism (nsSNPs) present in the Zinc-finger with UFM1-Specific Peptidase domain protein (ZUFSP) may be involved in genetic instability and carcinogenesis. For the first time, we employed in-silico approach using predictive tools to identify and validate potential nsSNPs that could be pathogenic. Our result revealed that 8 nsSNPs (rs 112738382, rs 140094037, rs 201652589, rs 201847265, rs 202076827, rs 373634906, rs 375114528, rs 772591104) are pathogenic after being subjected to rigorous filtering process. The structural impact of the nsSNPs on ZUFSP structure indicated that the nsSNPs affect the stability of the protein by lowering ZUFSP protein stability. Furthermore, conservation analysis showed that rs 201652589, rs 140094037, rs 201847265, and rs 772591104 were highly conserved. Interestingly, the protein-protein affinity between ZUFSP and Ubiquitin was altered rs 201652589, rs 140094037, rs 201847265, and rs 772591104 had a binding affinity of - 0.46, - 0.83, - 1.62, and - 1.12 kcal/mol respectively. Our study has been able to identify potential nsSNPs that could be used as genetic biomarkers for some diseases arising as a result of aberration in the ZUFSP structure, however, being a predictive study, the identified nsSNPs need to be experimentally investigated.
Collapse
Affiliation(s)
- Mary B Ajadi
- Department of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Howard Campus, Durban, 4000, South Africa
- Chemical Pathology Department, Faculty of Basic Medical Sciences, College of Health Sciences, Ladoke Akintola University of Technology, PMB 4400, Osogbo, Nigeria
| | - Opeyemi S Soremekun
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Adeniyi T Adewumi
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Hezekiel M Kumalo
- Department of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Howard Campus, Durban, 4000, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa.
| |
Collapse
|
4
|
Barik A, Katuwawala A, Hanson J, Paliwal K, Zhou Y, Kurgan L. DEPICTER: Intrinsic Disorder and Disorder Function Prediction Server. J Mol Biol 2019; 432:3379-3387. [PMID: 31870849 DOI: 10.1016/j.jmb.2019.12.030] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/07/2019] [Accepted: 12/15/2019] [Indexed: 01/06/2023]
Abstract
Computational predictions of the intrinsic disorder and its functions are instrumental to facilitate annotation for the millions of unannotated proteins. However, access to these predictors is fragmented and requires substantial effort to find them and to collect and combine their results. The DEPICTER (DisorderEd PredictIon CenTER) server provides first-of-its-kind centralized access to 10 popular disorder and disorder function predictions that cover protein and nucleic acids binding, linkers, and moonlighting regions. It automates the prediction process, runs user-selected methods on the server side, visualizes the results, and outputs all predictions in a consistent and easy-to-parse format. DEPICTER also includes two accurate consensus predictors of disorder and disordered protein binding. Empirical tests on an independent (low similarity) benchmark dataset reveal that the computational tools included in DEPICTER generate accurate predictions that are significantly better than the results secured using sequence alignment. The DEPICTER server is freely available at http://biomine.cs.vcu.edu/servers/DEPICTER/.
Collapse
Affiliation(s)
- Amita Barik
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, 23284, USA; Department of Biotechnology, National Institute of Technology, Durgapur, India
| | - Akila Katuwawala
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Jack Hanson
- Signal Processing Laboratory, Griffith University, Brisbane, QLD, 4122, Australia
| | - Kuldip Paliwal
- Signal Processing Laboratory, Griffith University, Brisbane, QLD, 4122, Australia
| | - Yaoqi Zhou
- School of Information and Communication Technology, Griffith University, Gold Coast, QLD, 4222, Australia; Institute for Glycomics, Griffith University, Gold Coast, QLD, 4222, Australia
| | - Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, 23284, USA.
| |
Collapse
|
5
|
Katayama T, Kawashima S, Okamoto S, Moriya Y, Chiba H, Naito Y, Fujisawa T, Mori H, Takagi T. TogoGenome/TogoStanza: modularized Semantic Web genome database. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2019; 2019:5277251. [PMID: 30624651 PMCID: PMC6323299 DOI: 10.1093/database/bay132] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 11/26/2018] [Indexed: 11/12/2022]
Abstract
TogoGenome is a genome database that is purely based on the Semantic Web technology, which enables the integration of heterogeneous data and flexible semantic searches.
All the information is stored as Resource Description Framework (RDF) data, and the reporting web pages are generated on the fly using SPARQL Protocol and RDF Query Language (SPARQL) queries. TogoGenome provides a semantic-faceted search system by gene functional annotation, taxonomy, phenotypes and environment based on the relevant ontologies. TogoGenome also serves as an interface to conduct semantic comparative genomics by which a user can observe pan-organism or organism-specific genes based on the functional aspect of gene annotations and the combinations of organisms from different taxa. The TogoGenome database exhibits a modularized structure, and each module in the report pages is separately served as TogoStanza, which is a generic framework for rendering an information block as IFRAME/Web Components, which can, unlike several other monolithic databases, also be reused to construct other databases. TogoGenome and TogoStanza have been under development since 2012 and are freely available along with their source codes on the GitHub repositories at https://github.com/togogenome/ and https://github.com/togostanza/, respectively, under the MIT license.
Collapse
Affiliation(s)
- Toshiaki Katayama
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Wakashiba, Kashiwa-shi, Chiba, Japan
| | - Shuichi Kawashima
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Wakashiba, Kashiwa-shi, Chiba, Japan
| | - Shinobu Okamoto
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Wakashiba, Kashiwa-shi, Chiba, Japan
| | - Yuki Moriya
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Wakashiba, Kashiwa-shi, Chiba, Japan
| | - Hirokazu Chiba
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Wakashiba, Kashiwa-shi, Chiba, Japan
| | - Yuki Naito
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Wakashiba, Kashiwa-shi, Chiba, Japan
| | | | - Hiroshi Mori
- National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Toshihisa Takagi
- National Institute of Genetics, Mishima, Shizuoka, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| |
Collapse
|
6
|
Blanco-Míguez A, Fdez-Riverola F, Sánchez B, Lourenço A. BlasterJS: A novel interactive JavaScript visualisation component for BLAST alignment results. PLoS One 2018; 13:e0205286. [PMID: 30300406 PMCID: PMC6177166 DOI: 10.1371/journal.pone.0205286] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/21/2018] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The wide range of potential applications has made the Basic Local Alignment Search Tool (BLAST) a ubiquitous tool in the field of Molecular Biology. Within this context, it is increasingly appealing to embed BLAST services within larger Web applications. RESULTS This work introduces BlasterJS viewer, a new JavaScript library for the lightweight development of Web-based applications supporting the visualisation of BLAST outputs. BlasterJS detaches from similar data viewers by focusing on the visual and interactive display of sequence similarity results and being completely independent of BLAST services. BlasterJS is compatible with the text outputs generated by the BLAST family of programs, namely BLASTp, BLASTn, BLASTx, tBLASTn, and tBLASTx, and works in all major Web browsers. Furthermore, BlasterJS is available through the EBI's BioJS registry 5, which extends its potential use to a wider scope of bioinformatics applications. CONCLUSIONS BlasterJS is new Javascript library that enables easy and seamless integration of visual and interactive representations of BLAST outputs in Web-based applications supporting sequence similarity search. BlasterJS is free accessible at http://sing-group.org/blasterjs/.
Collapse
Affiliation(s)
- Aitor Blanco-Míguez
- ESEI - Department of Computer Science, University of Vigo, Ourense, Spain
- CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Vigo, Spain
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Villaviciosa, Asturias, Spain
| | - Florentino Fdez-Riverola
- ESEI - Department of Computer Science, University of Vigo, Ourense, Spain
- CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Vigo, Spain
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Borja Sánchez
- CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Vigo, Spain
| | - Anália Lourenço
- ESEI - Department of Computer Science, University of Vigo, Ourense, Spain
- CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Vigo, Spain
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
| |
Collapse
|
7
|
Watkins X, Garcia LJ, Pundir S, Martin MJ. ProtVista: visualization of protein sequence annotations. Bioinformatics 2018; 33:2040-2041. [PMID: 28334231 PMCID: PMC5963392 DOI: 10.1093/bioinformatics/btx120] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Indexed: 11/22/2022] Open
Abstract
Summary: ProtVista is a comprehensive visualization tool for the graphical representation of protein sequence features in the UniProt Knowledgebase, experimental proteomics and variation public datasets. The complexity and relationships in this wealth of data pose a challenge in interpretation. Integrative visualization approaches such as provided by ProtVista are thus essential for researchers to understand the data and, for instance, discover patterns affecting function and disease associations. Availability and Implementation: ProtVista is a JavaScript component released as an open source project under the Apache 2 License. Documentation and source code are available at http://ebi-uniprot.github.io/ProtVista/. Contact:martin@ebi.ac.uk Supplementary information:Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Xavier Watkins
- EMBL-EBI, Hinxton, UK.,Open Targets Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | | | | | | | | |
Collapse
|
8
|
Horro C, Cook M, Attwood TK, Brazas MD, Hancock JM, Palagi P, Corpas M, Jimenez R. BioCIDER: a Contextualisation InDEx for biological Resources discovery. Bioinformatics 2017; 33:2607-2608. [PMID: 28407033 PMCID: PMC5870719 DOI: 10.1093/bioinformatics/btx213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/11/2017] [Indexed: 11/13/2022] Open
Abstract
Summary The vast, uncoordinated proliferation of bioinformatics resources (databases, software tools, training materials etc.) makes it difficult for users to find them. To facilitate their discovery, various services are being developed to collect such resources into registries. We have developed BioCIDER, which, rather like online shopping ‘recommendations’, provides a contextualization index to help identify biological resources relevant to the content of the sites in which it is embedded. Availability and Implementation BioCIDER (www.biocider.org) is an open-source platform. Documentation is available online (https://goo.gl/Klc51G), and source code is freely available via GitHub (https://github.com/BioCIDER). The BioJS widget that enables websites to embed contextualization is available from the BioJS registry (http://biojs.io/). All code is released under an MIT licence.
Collapse
Affiliation(s)
- Carlos Horro
- Elixir Department, Earlham Institute, Norwich Research Park Innovation Centre, Norwich NR4 7UH, UK
| | - Martin Cook
- ELIXIR Hub, The European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Teresa K Attwood
- School of Computer Science, The University of Manchester, Manchester M13 9PL, UK
| | - Michelle D Brazas
- Informatics and Bio-computing, Ontario Institute for Cancer Research, Toronto M5G 0A3, Canada
| | - John M Hancock
- Elixir Department, Earlham Institute, Norwich Research Park Innovation Centre, Norwich NR4 7UH, UK
| | - Patricia Palagi
- SIB Training Group, SIB Swiss Institute of Bioinformatics, Lausanne 1005, Switzerland
| | - Manuel Corpas
- Repositive, Future Business Centre, Kings' Hedges Road, Cambridge CB4 2HY, UK
| | - Rafael Jimenez
- ELIXIR Hub, The European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| |
Collapse
|
9
|
Jiménez RC, Kuzak M, Alhamdoosh M, Barker M, Batut B, Borg M, Capella-Gutierrez S, Chue Hong N, Cook M, Corpas M, Flannery M, Garcia L, Gelpí JL, Gladman S, Goble C, González Ferreiro M, Gonzalez-Beltran A, Griffin PC, Grüning B, Hagberg J, Holub P, Hooft R, Ison J, Katz DS, Leskošek B, López Gómez F, Oliveira LJ, Mellor D, Mosbergen R, Mulder N, Perez-Riverol Y, Pergl R, Pichler H, Pope B, Sanz F, Schneider MV, Stodden V, Suchecki R, Svobodová Vařeková R, Talvik HA, Todorov I, Treloar A, Tyagi S, van Gompel M, Vaughan D, Via A, Wang X, Watson-Haigh NS, Crouch S. Four simple recommendations to encourage best practices in research software. F1000Res 2017; 6. [PMID: 28751965 PMCID: PMC5490478 DOI: 10.12688/f1000research.11407.1] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/03/2017] [Indexed: 12/24/2022] Open
Abstract
Scientific research relies on computer software, yet software is not always developed following practices that ensure its quality and sustainability. This manuscript does not aim to propose new software development best practices, but rather to provide simple recommendations that encourage the adoption of existing best practices. Software development best practices promote better quality software, and better quality software improves the reproducibility and reusability of research. These recommendations are designed around Open Source values, and provide practical suggestions that contribute to making research software and its source code more discoverable, reusable and transparent. This manuscript is aimed at developers, but also at organisations, projects, journals and funders that can increase the quality and sustainability of research software by encouraging the adoption of these recommendations.
Collapse
Affiliation(s)
| | - Mateusz Kuzak
- Netherlands eScience Center, Science Park 140, Amsterdam, 1098 XG, Netherlands
| | - Monther Alhamdoosh
- CSL Limited, Bio21 Institute, 30 Flemington Road, Parkville, Victoria, 3010, Australia
| | - Michelle Barker
- National eResearch Collaboration Tools and Resources, Victoria, 3010, Australia
| | - Bérénice Batut
- ELIXIR-DE and de.NBI, Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Mikael Borg
- ELIXIR-SE, National Bioinformatics Infrastructure Sweden (NBIS), Scilifelab, Department of Biochemistry and Biophysics (DBB), Stockholm University, Stockholm, Sweden
| | - Salvador Capella-Gutierrez
- ELIXIR-ES, Spanish National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Almagro 3, Madrid, 28029, Spain
| | - Neil Chue Hong
- Software Sustainability Institute, JCMB, University of Edinburgh, Edinburgh, EH9 3FD, UK
| | - Martin Cook
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Manuel Corpas
- Repositive Ltd, Future Business Centre, Cambridge, UK
| | - Madison Flannery
- EMBL Australia Bioinformatics Resource, Lab-14, The University of Melbourne, 700 Swanston St, Parkville, Victoria, 3053, Australia
| | - Leyla Garcia
- EMBL-EBI, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Josep Ll Gelpí
- Barcelona Supercomputing Center, Barcelona, 08034, Spain.,Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, Barcelona, 08028, Spain
| | - Simon Gladman
- EMBL Australia Bioinformatics Resource, Lab-14, The University of Melbourne, 700 Swanston St, Parkville, Victoria, 3053, Australia
| | - Carole Goble
- ELIXIR-UK, Software Sustainability Institute, School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | | | | | - Philippa C Griffin
- EMBL Australia Bioinformatics Resource, Lab-14, The University of Melbourne, 700 Swanston St, Parkville, Victoria, 3053, Australia
| | - Björn Grüning
- ELIXIR-DE and de.NBI, Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Jonas Hagberg
- ELIXIR-SE, National Bioinformatics Infrastructure Sweden (NBIS), Scilifelab, Department of Biochemistry and Biophysics (DBB), Stockholm University, Stockholm, Sweden
| | - Petr Holub
- BBMRI-ERIC, Neue Stiftingtalstraße 2/B/6, Graz, 8010, Austria
| | - Rob Hooft
- Dutch TechCenter for Life Sciences and ELIXIR-NL, Utrecht, Netherlands
| | - Jon Ison
- ELIXIR-DK, Technical University of Denmark, Denmark, Denmark
| | - Daniel S Katz
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,School of Information Sciences, University of Illinois Urbana Champaign, Urbana, IL, USA.,Department of Electrical and Computer Engineering, University of Illinois Urbana Champaign, Urbana, IL, USA.,Department of Computer Science, University of Illinois Urbana Champaign, Urbana, IL, USA
| | - Brane Leskošek
- ELIXIR-SI, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | | | | | - David Mellor
- Center for Open Science, Charlottesville, VA, USA
| | | | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Robert Pergl
- ELIXIR-CZ, Faculty of Information Technology, Czech Technical University in Prague, Prague, Czech Republic
| | - Horst Pichler
- BBMRI.at, Alpen-Adria-University Klagenfurt, Klagenfurt, Austria
| | - Bernard Pope
- EMBL Australia Bioinformatics Resource, Lab-14, The University of Melbourne, 700 Swanston St, Parkville, Victoria, 3053, Australia
| | - Ferran Sanz
- GRIB, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Universitat Pompeu Fabra, Barcelona, Spain
| | - Maria V Schneider
- EMBL Australia Bioinformatics Resource, Lab-14, The University of Melbourne, 700 Swanston St, Parkville, Victoria, 3053, Australia
| | - Victoria Stodden
- School of Information Sciences, University of Illinois Urbana Champaign, Urbana, IL, USA
| | - Radosław Suchecki
- School of Agriculture, Food & Wine, University of Adelaide, Adelaide, Australia
| | - Radka Svobodová Vařeková
- Central European Institute of Technology (CEITEC), Brno, Czech Republic.,National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Harry-Anton Talvik
- ELIXIR-EE, Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Ilian Todorov
- Science & Technologies Facilities Council, Swindon, UK
| | | | - Sonika Tyagi
- EMBL Australia Bioinformatics Resource, Lab-14, The University of Melbourne, 700 Swanston St, Parkville, Victoria, 3053, Australia.,Australian Genome Research Facility Ltd., Melbourne, Australia
| | - Maarten van Gompel
- Centre for Language and Speech Technology, Radboud University Nijmegen, Nijmegen, Netherlands
| | | | - Allegra Via
- IBPM-CNR, Department of Biochemical Sciences , Sapienza University of Rome, Rome, Italy
| | - Xiaochuan Wang
- Faculty of Information Technology, Monash University, Victoria, Australia
| | | | - Steve Crouch
- Software Sustainability Institute, Web and Internet Science, University of Southampton, Southampton, UK
| |
Collapse
|
10
|
Ankenbrand MJ, Terhoeven N, Hohlfeld S, Förster F, Keller A. biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format. F1000Res 2017; 5:2348. [PMID: 28105307 PMCID: PMC5224677 DOI: 10.12688/f1000research.9618.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/09/2017] [Indexed: 11/20/2022] Open
Abstract
The Biological Observation Matrix (BIOM) format is widely used to store data from high-throughput studies. It aims at increasing interoperability of bioinformatic tools that process this data. However, due to multiple versions and implementation details, working with this format can be tricky. Currently, libraries in Python, R and Perl are available, whilst such for JavaScript are lacking. Here, we present a BioJS component for parsing BIOM data in all format versions. It supports import, modification, and export via a unified interface. This module aims to facilitate the development of web applications that use BIOM data. Finally, we demonstrate its usefulness by two applications that already use this component. Availability: https://github.com/molbiodiv/biojs-io-biom, https://dx.doi.org/10.5281/zenodo.218277.
Collapse
Affiliation(s)
- Markus J Ankenbrand
- Department of Animal Ecology and Tropical Biology (Zoology III), University of Würzburg, Würzburg, Germany
| | - Niklas Terhoeven
- Department of Plant Physiology and Biophysics (Botany I), University of Würzburg, Würzburg, Germany; Center for Computational and Theoretical Biology (CCTB), University of Würzburg, Würzburg, Germany
| | - Sonja Hohlfeld
- Department of Animal Ecology and Tropical Biology (Zoology III), University of Würzburg, Würzburg, Germany
| | - Frank Förster
- Center for Computational and Theoretical Biology (CCTB), University of Würzburg, Würzburg, Germany; Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Alexander Keller
- Department of Animal Ecology and Tropical Biology (Zoology III), University of Würzburg, Würzburg, Germany
| |
Collapse
|
11
|
Rauscher B, Heigwer F, Breinig M, Winter J, Boutros M. GenomeCRISPR - a database for high-throughput CRISPR/Cas9 screens. Nucleic Acids Res 2017; 45:D679-D686. [PMID: 27789686 PMCID: PMC5210668 DOI: 10.1093/nar/gkw997] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 10/12/2016] [Accepted: 10/14/2016] [Indexed: 12/12/2022] Open
Abstract
Over the past years, CRISPR/Cas9 mediated genome editing has developed into a powerful tool for modifying genomes in various organisms. In high-throughput screens, CRISPR/Cas9 mediated gene perturbations can be used for the systematic functional analysis of whole genomes. Discoveries from such screens provide a wealth of knowledge about gene to phenotype relationships in various biological model systems. However, a database resource to query results efficiently has been lacking. To this end, we developed GenomeCRISPR (http://genomecrispr.org), a database for genome-scale CRISPR/Cas9 screens. Currently, GenomeCRISPR contains data on more than 550 000 single guide RNAs (sgRNA) derived from 84 different experiments performed in 48 different human cell lines, comprising all screens in human cells using CRISPR/Cas published to date. GenomeCRISPR provides data mining options and tools, such as gene or genomic region search. Phenotypic and genome track views allow users to investigate and compare the results of different screens, or the impact of different sgRNAs on the gene of interest. An Application Programming Interface (API) allows for automated data access and batch download. As more screening data will become available, we also aim at extending the database to include functional genomic data from other organisms and enable cross-species comparisons.
Collapse
Affiliation(s)
- Benedikt Rauscher
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Department of Cell and Molecular Biology, Medical Faculty Mannheim, 69120 Heidelberg, Germany
| | - Florian Heigwer
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Department of Cell and Molecular Biology, Medical Faculty Mannheim, 69120 Heidelberg, Germany
| | - Marco Breinig
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Department of Cell and Molecular Biology, Medical Faculty Mannheim, 69120 Heidelberg, Germany
| | - Jan Winter
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Department of Cell and Molecular Biology, Medical Faculty Mannheim, 69120 Heidelberg, Germany
| | - Michael Boutros
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Department of Cell and Molecular Biology, Medical Faculty Mannheim, 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| |
Collapse
|
12
|
Affiliation(s)
- Mohamed Helmy
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | | | - Gary D. Bader
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- * E-mail:
| |
Collapse
|
13
|
Yachdav G, Wilzbach S, Rauscher B, Sheridan R, Sillitoe I, Procter J, Lewis SE, Rost B, Goldberg T. MSAViewer: interactive JavaScript visualization of multiple sequence alignments. Bioinformatics 2016; 32:3501-3503. [PMID: 27412096 PMCID: PMC5181560 DOI: 10.1093/bioinformatics/btw474] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 06/03/2016] [Accepted: 06/29/2016] [Indexed: 11/29/2022] Open
Abstract
Summary: The MSAViewer is a quick and easy visualization and analysis JavaScript component for Multiple Sequence Alignment data of any size. Core features include interactive navigation through the alignment, application of popular color schemes, sorting, selecting and filtering. The MSAViewer is ‘web ready’: written entirely in JavaScript, compatible with modern web browsers and does not require any specialized software. The MSAViewer is part of the BioJS collection of components. Availability and Implementation: The MSAViewer is released as open source software under the Boost Software License 1.0. Documentation, source code and the viewer are available at http://msa.biojs.net/. Supplementary information:Supplementary data are available at Bioinformatics online. Contact:msa@bio.sh
Collapse
Affiliation(s)
- Guy Yachdav
- Bioinformatik - I12, TUM, Garching, 85748, Germany.,Biosof LLC, New York, NY 10001, USA
| | | | | | - Robert Sheridan
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Ian Sillitoe
- Institute of Structure and Molecular Biology, University College London, London, UK
| | - James Procter
- Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK
| | | | - Burkhard Rost
- Bioinformatik - I12, TUM, Garching, 85748, Germany.,Biosof LLC, New York, NY 10001, USA
| | | |
Collapse
|
14
|
Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Grüning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li JW, Licata L, Mareuil F, Mičetić I, Friborg RM, Moretti S, Morris C, Möller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwämmle V, Smith C, Sperotto MM, Stockinger H, Vařeková RS, Tosatto SCE, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Løngreen P, Brunak S. Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res 2015; 44:D38-47. [PMID: 26538599 PMCID: PMC4702812 DOI: 10.1093/nar/gkv1116] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 10/13/2015] [Indexed: 01/24/2023] Open
Abstract
Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand. Here we present a community-driven curation effort, supported by ELIXIR—the European infrastructure for biological information—that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners. As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.
Collapse
Affiliation(s)
- Jon Ison
- Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark
| | - Kristoffer Rapacki
- Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark
| | - Hervé Ménager
- Centre d'Informatique pour la Biologie, C3BI, Institut Pasteur, France
| | - Matúš Kalaš
- Computational Biology Unit, Department of Informatics, University of Bergen, Norway
| | - Emil Rydza
- Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark
| | - Piotr Chmura
- Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark
| | - Christian Anthon
- Department of Veterinary Clinical and Animal Sciences, Faculty for Health and Medical Sciences, University of Copenhagen, Denmark
| | - Niall Beard
- School of Computer Science, University of Manchester, UK
| | - Karel Berka
- Department of Physical Chemistry, RCPTM, Faculty of Science, Palacky University, Czech Republic
| | - Dan Bolser
- The European Bioinformatics Institute (EMBL-EBI), UK
| | - Tim Booth
- NEBC Wallingford, Centre for Ecology and Hydrology, UK
| | - Anthony Bretaudeau
- INRA, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), France INRIA, IRISA, GenOuest Core Facility, France
| | - Jan Brezovsky
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Czech Republic
| | - Rita Casadio
- Bologna Biocomputing Group, University of Bologna, Italy
| | | | - Frederik Coppens
- Department of Plant Systems Biology, VIB, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium
| | | | | | - Kristian Davidsen
- Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark
| | | | - Tunca Dogan
- UniProt, European Bioinformatics Institute (EMBL-EBI), UK
| | | | - Laura Emery
- The European Bioinformatics Institute (EMBL-EBI), UK
| | | | - Thomas Gatter
- Faculty of Technology and Center for Biotechnology, Universität Bielefeld, Germany
| | | | - Marie Grosjean
- Institut Français de Bioinformatique (French Institute of Bioinformatics), CNRS, UMS3601, France
| | - Björn Grüning
- Albert-Ludwigs-Universität Freiburg, Fahnenbergplatz, 79085 Freiburg
| | | | - Hans Ienasescu
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Denmark
| | | | - Martin Closter Jespersen
- Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark
| | | | - Nick Juty
- The European Bioinformatics Institute (EMBL-EBI), UK
| | - Peter Juvan
- Centre for Functional Genomics and Biochips, Faculty of Medicine, University of Ljubljana, Slovenia
| | | | - Camille Laibe
- The European Bioinformatics Institute (EMBL-EBI), UK
| | - Jing-Woei Li
- Faculty of Medicine, The Chinese University of Hong Kong, China Hong Kong Bioinformatics Centre, School of Life Sciences,The Chinese University of Hong Kong, China
| | - Luana Licata
- Dept. of Biology, University of Rome Tor Vergata, Italy
| | - Fabien Mareuil
- Centre d'Informatique pour la Biologie, C3BI, Institut Pasteur, France
| | - Ivan Mičetić
- Department of Biomedical Sciences, University of Padua, Italy
| | | | - Sebastien Moretti
- SIB Swiss Institute of Bioinformatics, Switzerland Department of Ecology and Evolution, Biophore, Evolutionary Bioinformatics group, University of Lausanne, Switzerland
| | | | - Steffen Möller
- Department of Dermatology, University of Lübeck, Germany Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Germany
| | | | - Hedi Peterson
- Institute of Computer Science, University of Tartu, Estonia
| | | | - Peter Rice
- Department of Computing, William Penney Laboratory, Imperial College London, UK
| | | | | | - Rabie Saidi
- UniProt, European Bioinformatics Institute (EMBL-EBI), UK
| | | | - Veit Schwämmle
- Protein Research Group, Department for Biochemistry and Molecular Biology, University of Southern Denmark, Denmark
| | | | - Maria Maddalena Sperotto
- Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark
| | | | | | | | - Victor de la Torre
- National Bioinformatics Institute Unit (INB), Fundacion Centro Nacional de Investigaciones Oncologicas, Spain
| | | | - Allegra Via
- Dept. of Physics, Sapienza University, Italy
| | - Guy Yachdav
- Department of Informatics, Bioinformatics-I12, TUM, Germany
| | - Federico Zambelli
- Institute of Biomembranes and Bioenergetics, National Research Council (CNR), and Dept. of Biosciences, University of Milano, Italy
| | - Gert Vriend
- Radboud University Medical Centre, CMBI, Netherlands
| | - Burkhard Rost
- Department of Informatics, Bioinformatics-I12, TUM, Germany
| | | | - Peter Løngreen
- Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark
| | - Søren Brunak
- Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| |
Collapse
|
15
|
Yachdav G, Goldberg T, Wilzbach S, Dao D, Shih I, Choudhary S, Crouch S, Franz M, García A, García LJ, Grüning BA, Inupakutika D, Sillitoe I, Thanki AS, Vieira B, Villaveces JM, Schneider MV, Lewis S, Pettifer S, Rost B, Corpas M. Anatomy of BioJS, an open source community for the life sciences. eLife 2015; 4. [PMID: 26153621 PMCID: PMC4495654 DOI: 10.7554/elife.07009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 06/20/2015] [Indexed: 01/12/2023] Open
Abstract
BioJS is an open source software project that develops visualization tools for different types of biological data. Here we report on the factors that influenced the growth of the BioJS user and developer community, and outline our strategy for building on this growth. The lessons we have learned on BioJS may also be relevant to other open source software projects. DOI:http://dx.doi.org/10.7554/eLife.07009.001
Collapse
Affiliation(s)
- Guy Yachdav
- Bioinformatik, Biosof LLC, Garching, Germany
| | - Tatyana Goldberg
- Bioinformatik, Technische Universität München, Garching, Germany
| | | | - David Dao
- Bioinformatik, Technische Universität München, Garching, Germany
| | - Iris Shih
- Bioinformatik, Technische Universität München, Garching, Germany
| | - Saket Choudhary
- Molecular and Computational Biology, University of Southern California, Los Angeles, United States
| | - Steve Crouch
- Web and Internet Science, University of Southampton, Southampton, United Kingdom
| | - Max Franz
- Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | | | - Leyla J García
- European Molecular Biology Laboratory-European Bioinformatics Institute, Cambridge, United Kingdom
| | - Björn A Grüning
- Bioinformatics Group, Department of Computer Science and Centre for Biological Systems Analysis, University of Freiburg, Freiburg, Germany
| | - Devasena Inupakutika
- Web and Internet Science, University of Southampton, Southampton, United Kingdom
| | - Ian Sillitoe
- Institute of Structure and Molecular Biology, University College London, London, United Kingdom
| | | | - Bruno Vieira
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | | | | | - Suzanna Lewis
- Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Steve Pettifer
- School of Computer Science, The University of Manchester, Manchester, United Kingdom
| | | | | |
Collapse
|
16
|
Europe PMC: a full-text literature database for the life sciences and platform for innovation. Nucleic Acids Res 2014; 43:D1042-8. [PMID: 25378340 PMCID: PMC4383902 DOI: 10.1093/nar/gku1061] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
This article describes recent developments of Europe PMC (http://europepmc.org), the leading database for life science literature. Formerly known as UKPMC, the service was rebranded in November 2012 as Europe PMC to reflect the scope of the funding agencies that support it. Several new developments have enriched Europe PMC considerably since then. Europe PMC now offers RESTful web services to access both articles and grants, powerful search tools such as citation-count sort order and data citation features, a service to add publications to your ORCID, a variety of export formats, and an External Links service that enables any related resource to be linked from Europe PMC content.
Collapse
Affiliation(s)
- The Europe PMC Consortium
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- The British Library, 96 Euston Road, London NW1 2DB, UK
- Mimas, Roscoe Building, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
- National Centre for Text Mining, School of Computer Science, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
- To whom correspondence should be addressed. Johanna McEntyre. Tel: + 44 1223 492 599; Fax: + 44 1223 494 468;
| |
Collapse
|
17
|
Abstract
The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and 'dotifying' repeated amino acids. An option is also available to submit selected sequences to another web site, or to other JavaScript code. JSAV is implemented purely in JavaScript making use of the JQuery and JQuery-UI libraries. It does not use any HTML5-specific options to help with browser compatibility. The code is documented using JSDOC and is available from http://www.bioinf.org.uk/software/jsav/.
Collapse
Affiliation(s)
- Andrew C. R. Martin
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| |
Collapse
|
18
|
Meldal BHM, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S. The complex portal--an encyclopaedia of macromolecular complexes. Nucleic Acids Res 2014; 43:D479-84. [PMID: 25313161 PMCID: PMC4384031 DOI: 10.1093/nar/gku975] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The IntAct molecular interaction database has created a new, free, open-source, manually curated resource, the Complex Portal (www.ebi.ac.uk/intact/complex), through which protein complexes from major model organisms are being collated and made available for search, viewing and download. It has been built in close collaboration with other bioinformatics services and populated with data from ChEMBL, MatrixDB, PDBe, Reactome and UniProtKB. Each entry contains information about the participating molecules (including small molecules and nucleic acids), their stoichiometry, topology and structural assembly. Complexes are annotated with details about their function, properties and complex-specific Gene Ontology (GO) terms. Consistent nomenclature is used throughout the resource with systematic names, recommended names and a list of synonyms all provided. The use of the Evidence Code Ontology allows us to indicate for which entries direct experimental evidence is available or if the complex has been inferred based on homology or orthology. The data are searchable using standard identifiers, such as UniProt, ChEBI and GO IDs, protein, gene and complex names or synonyms. This reference resource will be maintained and grow to encompass an increasing number of organisms. Input from groups and individuals with specific areas of expertise is welcome.
Collapse
Affiliation(s)
- Birgit H M Meldal
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Oscar Forner-Martinez
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Maria C Costanzo
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5477, USA
| | - Jose Dana
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Janos Demeter
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5477, USA
| | - Marine Dumousseau
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Selina S Dwight
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5477, USA
| | - Anna Gaulton
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Luana Licata
- Department of Biology, University of Rome, Tor Vergata, Rome 00133, Italy
| | - Anna N Melidoni
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Sylvie Ricard-Blum
- UMR 5086 CNRS, Université Lyon1, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, 69367 Lyon Cedex 07, France
| | - Bernd Roechert
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland
| | - Marek S Skyzypek
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5477, USA
| | - Manu Tiwari
- Stammzellbiologie, Institut für Anatomie und Zellbiologie, GZMB Universitätsmedizin Göttingen, Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Sameer Velankar
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Edith D Wong
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5477, USA
| | - Henning Hermjakob
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Sandra Orchard
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| |
Collapse
|
19
|
Abstract
Data-driven research has gained momentum in the life sciences. Visualisation of these data is essential for quick generation of hypotheses and their translation into useful knowledge. BioJS is a new proposed standard for JavaScript-based components to visualise biological data. BioJS is an open source community project that to date provides 39 different components contributed by a global community. Here, we present the BioJS F1000Research collection series. A total of 12 components and a project status article are published in bulk. This collection does not intend to be an all-encompassing, comprehensive source of BioJS articles, but an initial set; future submissions from BioJS contributors are welcome.
Collapse
Affiliation(s)
- Manuel Corpas
- The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| |
Collapse
|