Hervé Ménager

Mobyle: a new full web bioinformatics framework.

Motivation: For the biologist, running bioinformatics analyses involves a time-consuming management of data and tools. Users need support to organize their work, retrieve parameters and reproduce their analyses. They also need to be able to combine their analytic tools using a safe data flow software mechanism. Finally, given that scientific tools can be difficult to install, it is particularly helpful for biologists to be able to use these tools through a web user interface. However, providing a web interface for a set of tools raises the problem that a single web portal cannot offer all the existing and possible services: it is the user, again, who has to cope with data copy among a number of different services. A framework enabling portal administrators to build a network of cooperating services would therefore clearly be beneficial. Results: We have designed a system, Mobyle, to provide a flexible and usable Web environment for defining and running bioinformatics analyses. It embeds simple yet powerful data management features that allow the user to reproduce analyses and to combine tools using a hierarchical typing system. Mobyle offers invocation of services distributed over remote Mobyle servers, thus enabling a federated network of curated bioinformatics portals without the user having to learn complex concepts or to install sophisticated software. While being focused on the end user, the Mobyle system also addresses the need, for the bioinfomatician, to automate remote services execution: PlayMOBY is a companion tool that automates the publication of BioMOBY web services, using Mobyle program definitions. Availability: The Mobyle system is distributed under the terms of the GNU GPLv2 on the project web site (http://bioweb2.pasteur.fr/projects/mobyle/). It is already deployed on three servers: http://mobyle.pasteur.fr, http://mobyle.rpbs.univ-paris-diderot.fr and http://lipm-bioinfo.toulouse.inra.fr/Mobyle. The PlayMOBY companion is distributed under the terms of the CeCILL license, and is available at http://lipm-bioinfo.toulouse.inra.fr/biomoby/PlayMOBY/. Contact: mobyle-support@pasteur.fr; mobyle-support@rpbs.univ-paris-diderot.fr; letondal@pasteur.fr Supplementary information:Supplementary data are available at Bioinformatics online.

Tools and data services registry: a community effort to document bioinformatics resources

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.

MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems

Motivation Biologists often wish to use their knowledge on a few experimental models of a given molecular system to identify homologs in genomic data. We developed a generic tool for this purpose. Results Macromolecular System Finder (MacSyFinder) provides a flexible framework to model the properties of molecular systems (cellular machinery or pathway) including their components, evolutionary associations with other systems and genetic architecture. Modelled features also include functional analogs, and the multiple uses of a same component by different systems. Models are used to search for molecular systems in complete genomes or in unstructured data like metagenomes. The components of the systems are searched by sequence similarity using Hidden Markov model (HMM) protein profiles. The assignment of hits to a given system is decided based on compliance with the content and organization of the system model. A graphical interface, MacSyView, facilitates the analysis of the results by showing overviews of component content and genomic context. To exemplify the use of MacSyFinder we built models to detect and class CRISPR-Cas systems following a previously established classification. We show that MacSyFinder allows to easily define an accurate “Cas-finder” using publicly available protein profiles. Availability and Implementation MacSyFinder is a standalone application implemented in Python. It requires Python 2.7, Hmmer and makeblastdb (version 2.2.28 or higher). It is freely available with its source code under a GPLv3 license at https://github.com/gem-pasteur/macsyfinder. It is compatible with all platforms supporting Python and Hmmer/makeblastdb. The “Cas-finder” (models and HMM profiles) is distributed as a compressed tarball archive as Supporting Information.

Semantic Map of Services for Structural Bioinformatics

We present a semantic map of resources for structural bioinformatics applied to proteins, i.e., various methods to predict and analyze protein structures in silico. Our map depicts resources on two levels: a logical level that provides a high-level description of the scientific concepts using a domain ontology; a physical level, that describes the actual resources implementing these connections. Scientists can use our system to express a query that captures their scientific aim, and are guided to identify the resources best meeting their needs. It is intended to provide scientists a tool to register and share knowledge about the available services in this field. Our approach addresses the problem of semantic interoperability of scientific resources publicly available on the Web

BioShaDock: a community driven bioinformatics shared Docker-based tools registry

Linux container technologies, as represented by Docker, provide an alternative to complex and time-consuming installation processes needed for scientific software. The ease of deployment and the process isolation they enable, as well as the reproducibility they permit across environments and versions, are among the qualities that make them interesting candidates for the construction of bioinformatic infrastructures, at any scale from single workstations to high throughput computing architectures. The Docker Hub is a public registry which can be used to distribute bioinformatic software as Docker images. However, its lack of curation and its genericity make it difficult for a bioinformatics user to find the most appropriate images needed. BioShaDock is a bioinformatics-focused Docker registry, which provides a local and fully controlled environment to build and publish bioinformatic software as portable Docker images. It provides a number of improvements over the base Docker registry on authentication and permissions management, that enable its integration in existing bioinformatic infrastructures such as computing platforms. The metadata associated with the registered images are domain-centric, including for instance concepts defined in the EDAM ontology, a shared and structured vocabulary of commonly used terms in bioinformatics. The registry also includes user defined tags to facilitate its discovery, as well as a link to the tool description in the ELIXIR registry if it already exists. If it does not, the BioShaDock registry will synchronize with the registry to create a new description in the Elixir registry, based on the BioShaDock entry metadata. This link will help users get more information on the tool such as its EDAM operations, input and output types. This allows integration with the ELIXIR Tools and Data Services Registry, thus providing the appropriate visibility of such images to the bioinformatics community.

SemanticBio: building conceptual scientific workflows over web services

We introduce here the SemanticBio system, which allows expressing scientific protocols as workflows that manipulate scientific objects represented in an ontology. The different tasks are executed using web services, which address many interoperability issues, and are available as interfaces to a variety of life science resources.

Using registries to integrate bioinformatics tools and services into workbench environments

The diversity and complexity of bioinformatics resources presents significant challenges to their localisation, deployment and use, creating a need for reliable systems that address these issues. Meanwhile, users demand increasingly usable and integrated ways to access and analyse data, especially within convenient, integrated “workbench” environments. Resource descriptions are the core element of registry and workbench systems, which are used to both help the user find and comprehend available software tools, data resources, and Web Services, and to localise, execute and combine them. The descriptions are, however, hard and expensive to create and maintain, because they are volatile and require an exhaustive knowledge of the described resource, its applicability to biological research, and the data model and syntax used to describe it. We present here the Workbench Integration Enabler, a software component that will ease the integration of bioinformatics resources in a workbench environment, using their description provided by the existing ELIXIR Tools and Data Services Registry.

Semantic map for structural bioinformatics: enhanced service discovery based on high level concept ontology

The amount of bioinformatics services available over the web has dramatically increased over the last years. Generalist on-line catalogs help identifying a particular service in such a pool. Unfortunately, most of the time, querying those catalogs is only based on a textual search for a particular datatype or a domain of interest. In this context, we have developed the Structural Bioinformatics Semantic Map (SBMap), a dual level ontology that allows users to discover structural bioinformatics resources through the exploration of a graph of high level concepts. In this paper, we present how participative design workshops helped us to improve the navigation experiment. The SBMap discovery tool (release-candidate) is available at: http://sbmap.rpbs.univ-paris-diderot.fr

Bioinformatics applications discovery and composition with the mobyle suite and mobylenet

Given the sheer number of existing analysis tools and data sources, defining and running bioinformatics analyses is often challenging. We present here the Mobyle framework, a web-based environment to access such resources. It enables the use of local and remote bioinformatics services, seamlessly integrated within a homogeneous and web-accessible environment that focuses on usability. This framework offers the possibility of integrating a wide range of services that span from the traditional server-side command-line based programs to workflows and client-based visualization tools. By abstracting whenever possible the user from the details of syntactic compatibility and providing multiple classification tools, Mobyle provides an efficient web-based solution to run and chain bioinformatics analyses. The MobyleNet project promotes an organization that federates a network of small resources that shares its expertise within a community that spans various complementary domains of bioinformatics. Its most tangible expected result is the integration of the bioinformatics tools of the different nodes, providing interoperability, user assistance and quality management between its members.

A Workflow Engine for the Execution of Scientific Protocols

We present the execution engine of the SemanticBio system, an integration solution that provides scientists support to express and execute scientific protocols. In SemanticBio scientific workflows are first expressed as conceptual workflows using scientific ontologies. Conceptual workflows are then translated in a semi-automated process into executable workflows, composed of calls to coordinated web services. Once the user has selected an executable workflow that meets the protocol needs, the SemanticBio execution engine supports the execution of data flow-coordinated tasks, i.e., the execution of a task is only based on the availability of its inputs. This engine is a lightweight, yet flexible approach to the execution of such workflows. Our approach addresses the problem of semantic interoperability of scientific resources publicly available on the web.