The bio.tools registry of software tools and data resources for the life sciences

Ison, Jon C.; Ienasescu, Hans; Chmura, Piotr Jaroslaw; Rydza, Emil Karol; Ménager, Hervé; Kalaš, Matúš; Schwämmle, Veit; Grüning, Björn; Beard, Niall; López, Rodrigo; Duvaud, Séverine; Stockinger, Heinz; Persson, Bengt; Svobodová, Radka; Raček, Tomáš; Vondrášek, Jiřı́; Peterson, Hedi; Salumets, Ahto; Jonassen, Inge; Hooft, Rob; Nyrönen, Tommi; Valencia, Alfonso; Capella, Salvador; Gelpi, Josep L. L.; Zambelli, Federico; Savakis, Babis; Leskošek, Brane; Rapacki, Kristoffer; Blanchet, Christophe; Jiménez, Rafael C.; Oliveira, Arlindo L.; Vriend, Gert; Collin, Olivier; Helden, Jacques van; Løngreen, Peter; Brunak, Søren

doi:10.1186/s13059-019-1772-6

Cited by 57 publications

(46 citation statements)

References 22 publications

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“…There are currently multiple projects working on concrete solutions to add structured metadata annotations to software. Examples include the biotoolsSchema [26], a formalised schema (XSD) used by the bio.tools project [27,28]; the CodeMeta set of terms [29] and Bioschemas Tool profile [30]. The latter two work on top of schema.org, a project aiming to make it easier to add structured markup to web pages, and help search engines to index them.…”

Section: F2 Data Are Described With Rich Metadatamentioning

confidence: 99%

Towards FAIR principles for research software

Lamprecht

García

Kuzak

et al. 2020

Self Cite

224

190

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Section: F2 Data Are Described With Rich Metadatamentioning

confidence: 99%

Towards FAIR principles for research software

Lamprecht

García

Kuzak

et al. 2020

Self Cite

224

190

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show abstract

“…Websites and publications were retrieved from bio.tools ( 26 ) and PubMed. We downloaded all tools listed as ‘Web service’, ‘Web API’, ‘Web application’, ‘Bioinformatics portal’ and ‘Database portal’ from the bio.tools website (latest updated on 2021-02-09) and kept all entries that could be linked to a publication (either with a PMID or with a DOI that could be converted to a PMID).…”

Section: Methodsmentioning

confidence: 99%

Aviator: a web service for monitoring the availability of web services

Fehlmann

Kern

Hirsch

et al. 2021

Nucleic Acids Research

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With Aviator, we present a web service and repository that facilitates surveillance of online tools. Aviator consists of a user-friendly website and two modules, a literature-mining based general and a manually curated module. The general module currently checks 9417 websites twice a day with respect to their availability and stores many features (frontend and backend response time, required RAM and size of the web page, security certificates, analytic tools and trackers embedded in the webpage and others) in a data warehouse. Aviator is also equipped with an analysis functionality, for example authors can check and evaluate the availability of their own tools or those of their peers. Likewise, users can check the availability of a certain tool they intend to use in research or teaching to avoid including unstable tools. The curated section of Aviator offers additional services. We provide API snippets for common programming languages (Perl, PHP, Python, JavaScript) as well as an OpenAPI documentation for embedding in the backend of own web services for an automatic test of their function. We query the respective APIs twice a day and send automated notifications in case of an unexpected result. Naturally, the same analysis functionality as for the literature-based module is available for the curated section. Aviator can freely be used at https://www.ccb.uni-saarland.de/aviator.

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“…Similar initiatives exist, either for a broader range of applications, for example bio.tools , 18 , 19 which has gathered more than 20000 software tools in the full range of life science applications, or for more specific application topics, for example Quantitative Plant , which focusses on tools for the analysis of image data of plants 20 or BioImage.io for pre trained AI deep learning models.…”

Section: Finding Workflows or Components For A Specific Biological Problem Or Taskmentioning

confidence: 99%

Bioimage analysis workflows: community resources to navigate through a complex ecosystem

et al. 2021

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Workflows are the keystone of bioimage analysis, and the NEUBIAS (Network of European BioImage AnalystS) community is trying to gather the actors of this field and organize the information around them. One of its most recent outputs is the opening of the F1000Research NEUBIAS gateway, whose main objective is to offer a channel of publication for bioimage analysis workflows and associated resources. In this paper we want to express some personal opinions and recommendations related to finding, handling and developing bioimage analysis workflows. The emergence of "big data” in bioimaging and resource-intensive analysis algorithms make local data storage and computing solutions a limiting factor. At the same time, the need for data sharing with collaborators and a general shift towards remote work, have created new challenges and avenues for the execution and sharing of bioimage analysis workflows. These challenges are to reproducibly run workflows in remote environments, in particular when their components come from different software packages, but also to document them and link their parameters and results by following the FAIR principles (Findable, Accessible, Interoperable, Reusable) to foster open and reproducible science. In this opinion paper, we focus on giving some directions to the reader to tackle these challenges and navigate through this complex ecosystem, in order to find and use workflows, and to compare workflows addressing the same problem. We also discuss tools to run workflows in the cloud and on High Performance Computing resources, and suggest ways to make these workflows FAIR.

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The bio.tools registry of software tools and data resources for the life sciences

Cited by 57 publications

References 22 publications

Towards FAIR principles for research software

Towards FAIR principles for research software

Aviator: a web service for monitoring the availability of web services

Bioimage analysis workflows: community resources to navigate through a complex ecosystem

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