WAVES

Notes given in the application form

Eligibility criteria

  • Must be an ELIXIR Service (i.e. part of an existing ELIXIR Node’s Service Delivery Plan, or is an ELIXIR Commissioned Service), or is in the official process/commitment of becoming one. (Required)
  • Must have evidence that it supports an interoperability activity, and has been deployed. (Required)
  • Must indicate how it supports the FAIR Principles. (Required)
  • Should fit into the EIP service framework in the ELIXIR 2019-2023 Scientific Programme for data interoperability or other activities relevant to the ELIXIR mission.

Additional notes

  • Please complete this form by adding information for your Interoperability Resource in the appropriate section below. Consult with Recommended Interoperability Resource (RIR) selection criteria documentation on details for each section below.
  • Where a panel/question is not relevant to your Interoperability Resource, please leave it blank or mark as “not applicable”, optionally with a brief explanation as to why.
  • Word limit guidance is noted for free text fields.
  • Please include urls to external resources, where useful.
  • Any questions, contact Sirarat Sarntivijai (sirarat.sarntivijai@elixir-europe.org).

1. Resource facilitation to scientific research

a. Interoperability Resource: Briefly describe the function of the Interoperability Resource

WAVES is a web application dedicated to bioinformatic tool integration. It provides an efficient way to implement a service for any bioinformatic software. Such services are automatically made available in three ways: web pages, web forms to include in remote websites, and a RESTful web services API to access remotely from applications. In order to fulfill the service’s computational needs, WAVES can perform computation on various resources and environments, such as Galaxy instances.

b. Scope statement: describe the scope , and the users of the resource. How is the Interoperability Resource positioned with respect to other similar Interoperability Resources? Include the base URL and, if relevant, the introductory or “about” page URL.

WAVES is a web application based on a service-oriented architecture, intended to be used as a service provider platform. There are three different ways to interact with WAVES services: web pages, web forms and a RESTful API. WAVES automatically creates a web page for each integrated tool. In the same manner, it generates web forms to be directly integrated into any website. Lastly, WAVES provides web service entries in its RESTful API, thus generating services suitable for software interoperability. These web services all share the same API structure which complies to the Core API standard (http://www.coreapi.org/).

Moreover, the web pages and the web forms generated by WAVES include metadata (based on schema.org) that describe the service, thus ensuring the findability of the services.

WAVES is intended to be used by any bioinformaticians in charge of website implementation, thus creating a standardized interoperability layer over any integrated tool.

c. Resource url

http://www.atgc-montpellier.fr/waves/

d. Inter-organisational recognition: does the Interoperability Resource have community recognition? (e.g. demonstrated through a collaboration, geographical diversity in the source of the submissions, international diversity of delivery partners and/or funders)

WAVES was developed recently and published in 2019 (https://doi.org/10.1093/bioinformatics/bty639). Thus, its Life Cycle stage is ‘Emerging’. However, it is already used by two french platforms involved in the French ELIXIR node : the CBIB in Bordeaux and ATGC in Montpellier.

2. Community

a. Community impact: If applicable, provide documented evidence of community impact (e.g., publication citations, API calls, projects using the resource, etc.)

At ATGC, we are developing a platform of services dedicated to phylogenomic analyzes, in the same spirit of NGphylogeny.fr (https://doi.org/10.1093/nar/gkz303). It involves developing a server offering application workflows with a high-level interface integrating the tools that make reference in the field and that correspond to the needs of biologists. In this project, we use WAVES 1/ to integrate the bioinformatic programs, 2/ to generate the web forms and 3/ to manage the computations.

At CBIB, they use WAVES to provide the biologists access through web pages to the programs and pipelines they develop.

b. Potential usage: Describe other systems that could use this candidate resource, but currently do not.

Every web server that provide bioinformatic analysis services could benefit of the usage of WAVES to improve its findability and interoperability. By using WAVES, it is straightforward to set up interoperable and findable web pages and web forms for running online bioinformatic software.

c. Outreach & support: Provide resource support publication(s)/user documentation(s) describing the Interoperability Resource (e.g. scientific journal publications, community preprints, resource user’s documentations etc.), resource dissemination plan (e.g. workshops, conference presentations), and other equal-opportunity research support (if applicable).

All resources concerning WAVES are available from its main page:
http://www.atgc-montpellier.fr/waves/

This includes:

We organized three trainings for the French bioinformatic platforms to promote the usage of WAVES : http://www.atgc-montpellier.fr/waves/trainings.php. Each training involved about 10 people.

d. Dependency of other resources: How is this resource critical to the user(s)? Do other resources depend on the resource described here to provide downstream service? Please list, or provide a link to a diagram.

 

3. Quality of resource

a. Uptime: Average percentage uptime/month during the last 12 months, response time of the resource. In case of ontology/standards production, interval of update/release, adaptability of ontology design patterns to evolving data. Provide information where applicable: uptime of resource, software release cycle (please state week/month etc), update frequency.

In 2017, WAVES was still in developement stage, thus we released 10 versions, from 1.1 to 1.5. At the beginning of 2018, we released the version 1.6, which had some minor revisions to reach the version 1.6.7 in january 2020. The release history is available from GitHub:
https://github.com/lirmm/waves-core/releases

b. Accessibility: what are resource retrieval mechanisms? Does the resource provide web-based user interface, application programmable interface (API), containers, and/or other channels? Please list resource access mechanism, provide URLs as applicable.

The main WAVES functionality is to automatically generate web-based user interface (web page and web form) and API for each integrated service.

c. Maintenance quality: Is there a maintenance SOP or plan, reflecting sustainability and scalability? Does it align with guidelines for sustainable software development? Please include a resource commitment statement (description text or URL).

WAVES is part of the software developed and maintained within ATGC platform (http://www.atgc-montpellier.fr/). We are developping a new version of the ATGC website based on 1/ a CMS to manage the content and 2/ WAVES to manage the computations. We are also developping a web server dedicated to phylogenomic analysis which is based on WAVES (see above). Thus WAVES will be maintained by the ATGC staff.

d. Support quality: Please list support mechanisms (e.g., point of contact, request ticketing, resource’s response time where a solution is identified, etc.), and methods to collect user feedback. If available, list tutorial documentations or tutorial materials and format, including linking on the ELIXIR’s Training Portal (TeSS) (or other training platforms) where applicable.

We use the issues management system from GitHub to follow up:
https://github.com/lirmm/waves-core/issues

We organized three trainings (in French) dedicated to WAVES for about 30 people.

4. Legal framework, funding, and governance

a. Legal framework: What are the resource’s license/terms of use? Can the license facilitate Open Science? Please include the url for the license the resource uses.

WAVES is licensed under GPLv3. The source code is open.

b. Privacy/Ethics policy: If applicable, is there a publicly available privacy policy in which use and security around personal data are described (e.g. the EU General Data Protection Regulation (GDPR), ELIXIR Ethics Policy, other relevant ELIXIR Policies)? Please include the url of the privacy/ethics policy, if applicable.

The terms of use are available here: http://www.atgc-montpellier.fr/index.php?type=tou

c. Funding & sustainability plan: List of funding sources supporting the resource, and sustainability plan.

The development of WAVES was supported by IFB, the French node of ELIXIR.

d. Governance: Describe the Resource’s QA/QC plan that guarantees similar quality governance to that of ELIXIR. Please link SAB members, if applicable.