Seahawk: moving beyond HTML in Web-based bioinformatics analysis

mORCA: ubiquitous access to life science web services

Background

Technical advances in mobile devices such as smartphones and tablets have produced an extraordinary increase in their use around the world and have become part of our daily lives. The possibility of carrying these devices in a pocket, particularly mobile phones, has enabled ubiquitous access to Internet resources. Furthermore, in the life sciences world there has been a vast proliferation of data types and services that finish as Web Services. This suggests the need for research into mobile clients to deal with life sciences applications for effective usage and exploitation.

Results

Analysing the current features in existing bioinformatics applications managing Web Services, we have devised, implemented, and deployed an easy-to-use web-based lightweight mobile client. This client is able to browse, select, compose parameters, invoke, and monitor the execution of Web Services stored in catalogues or central repositories. The client is also able to deal with huge amounts of data between external storage mounts. In addition, we also present a validation use case, which illustrates the usage of the application while executing, monitoring, and exploring the results of a registered workflow. The software its available in the Apple Store and Android Market and the source code is publicly available in Github.

Conclusions

Mobile devices are becoming increasingly important in the scientific world due to their strong potential impact on scientific applications.

Bioinformatics should not fall behind this trend. We present an original software client that deals with the intrinsic limitations of such devices and propose different guidelines to provide location-independent access to computational resources in bioinformatics and biomedicine. Its modular design makes it easily expandable with the inclusion of new repositories, tools, types of visualization, etc.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4439-x) contains supplementary material, which is available to authorized users.

Designing integrated computational biology pipelines visually

The long-term cost of developing and maintaining a computational pipeline that depends upon data integration and sophisticated workflow logic is too high to even contemplate "what if" or ad hoc type queries. In this paper, we introduce a novel application building interface for computational biology research, called VizBuilder, by leveraging a recent query language called BioFlow for life sciences databases. Using VizBuilder, it is now possible to develop ad hoc complex computational biology applications at throw away costs. The underlying query language supports data integration and workflow construction almost transparently and fully automatically, using a best effort approach. Users express their application by drawing it with VizBuilder icons and connecting them in a meaningful way. Completed applications are compiled and translated as BioFlow queries for execution by the data management system LifeDB, for which VizBuilder serves as a front end. We discuss VizBuilder features and functionalities in the context of a real life application after we briefly introduce BioFlow. The architecture and design principles of VizBuilder are also discussed. Finally, we outline future extensions of VizBuilder. To our knowledge, VizBuilder is a unique system that allows visually designing computational biology pipelines involving distributed and heterogeneous resources in an ad hoc manner.

The Bluejay genome browser

The Bluejay genome browser is a stand-alone visualization tool for the multi-scale viewing of annotated genomes and other genomic elements. Bluejay allows users to customize display features to suit their needs, and produces publication-quality graphics. Bluejay provides a multitude of ways to interrelate biological data at the genome scale. Users can load gene expression data into a genome display for expression visualization in context. Multiple genomes can be compared concurrently, including time series expression data, based on Gene Ontology labels. External, context-sensitive biological Web Services are linked to the displayed genomic elements ad hoc for in-depth genomic data analysis and interpretation. Users can mark multiple points of interest in a genome by creating waypoints, and exploit them for easy navigation of single or multiple genomes. Using this comprehensive visual environment, users can study a gene not just in relation to its genome, but also its transcriptome and evolutionary origins. Written in Java, Bluejay is platform-independent and is freely available from http://bluejay.ucalgary.ca.

KBWS: an EMBOSS associated package for accessing bioinformatics web services

The availability of bioinformatics web-based services is rapidly proliferating, for their interoperability and ease of use. The next challenge is in the integration of these services in the form of workflows, and several projects are already underway, standardizing the syntax, semantics, and user interfaces. In order to deploy the advantages of web services with locally installed tools, here we describe a collection of proxy client tools for 42 major bioinformatics web services in the form of European Molecular Biology Open Software Suite (EMBOSS) UNIX command-line tools. EMBOSS provides sophisticated means for discoverability and interoperability for hundreds of tools, and our package, named the Keio Bioinformatics Web Service (KBWS), adds functionalities of local and multiple alignment of sequences, phylogenetic analyses, and prediction of cellular localization of proteins and RNA secondary structures. This software implemented in C is available under GPL from http://www.g-language.org/kbws/ and GitHub repository http://github.com/cory-ko/KBWS. Users can utilize the SOAP services implemented in Perl directly via WSDL file at http://soap.g-language.org/kbws.wsdl (RPC Encoded) and http://soap.g-language.org/kbws_dl.wsdl (Document/literal).

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*

Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies.

XML-based approaches for the integration of heterogeneous bio-molecular data

Background

The today's public database infrastructure spans a very large collection of heterogeneous biological data, opening new opportunities for molecular biology, bio-medical and bioinformatics research, but raising also new problems for their integration and computational processing.

Results

In this paper we survey the most interesting and novel approaches for the representation, integration and management of different kinds of biological data by exploiting XML and the related recommendations and approaches. Moreover, we present new and interesting cutting edge approaches for the appropriate management of heterogeneous biological data represented through XML.

Conclusion

XML has succeeded in the integration of heterogeneous biomolecular information, and has established itself as the syntactic glue for biological data sources. Nevertheless, a large variety of XML-based data formats have been proposed, thus resulting in a difficult effective integration of bioinformatics data schemes. The adoption of a few semantic-rich standard formats is urgent to achieve a seamless integration of the current biological resources.

Magallanes: a web services discovery and automatic workflow composition tool

Background

To aid in bioinformatics data processing and analysis, an increasing number of web-based applications are being deployed. Although this is a positive circumstance in general, the proliferation of tools makes it difficult to find the right tool, or more importantly, the right set of tools that can work together to solve real complex problems.

Results

Magallanes (Magellan) is a versatile, platform-independent Java library of algorithms aimed at discovering bioinformatics web services and associated data types. A second important feature of Magallanes is its ability to connect available and compatible web services into workflows that can process data sequentially to reach a desired output given a particular input. Magallanes' capabilities can be exploited both as an API or directly accessed through a graphic user interface.

The Magallanes' API is freely available for academic use, and together with Magallanes application has been tested in MS-Windows™ XP and Unix-like operating systems. Detailed implementation information, including user manuals and tutorials, is available at .

Conclusion

Different implementations of the same client (web page, desktop applications, web services, etc.) have been deployed and are currently in use in real installations such as the National Institute of Bioinformatics (Spain) and the ACGT-EU project. This shows the potential utility and versatility of the software library, including the integration of novel tools in the domain and with strong evidences in the line of facilitate the automatic discovering and composition of workflows.

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.

Solutions for data integration in functional genomics: a critical assessment and case study

The torrent of data emerging from the application of new technologies to functional genomics and systems biology can no longer be contained within the traditional modes of data sharing and publication with the consequence that data is being deposited in, distributed across and disseminated through an increasing number of databases. The resulting fragmentation poses serious problems for the model organism community which increasingly rely on data mining and computational approaches that require gathering of data from a range of sources. In the light of these problems, the European Commission has funded a coordination action, CASIMIR (coordination and sustainability of international mouse informatics resources), with a remit to assess the technical and social aspects of database interoperability that currently prevent the full realization of the potential of data integration in mouse functional genomics. In this article, we assess the current problems with interoperability, with particular reference to mouse functional genomics, and critically review the technologies that can be deployed to overcome them. We describe a typical use-case where an investigator wishes to gather data on variation, genomic context and metabolic pathway involvement for genes discovered in a genome-wide screen. We go on to develop an automated approach involving an in silico experimental workflow tool, Taverna, using web services, BioMart and MOLGENIS technologies for data retrieval. Finally, we focus on the current impediments to adopting such an approach in a wider context, and strategies to overcome them.

Bluejay 1.0: genome browsing and comparison with rich customization provision and dynamic resource linking

Background

The Bluejay genome browser has been developed over several years to address the challenges posed by the ever increasing number of data types as well as the increasing volume of data in genome research. Beginning with a browser capable of rendering views of XML-based genomic information and providing scalable vector graphics output, we have now completed version 1.0 of the system with many additional features. Our development efforts were guided by our observation that biologists who use both gene expression profiling and comparative genomics gain functional insights above and beyond those provided by traditional per-gene analyses.

Results

Bluejay 1.0 is a genome viewer integrating genome annotation with: (i) gene expression information; and (ii) comparative analysis with an unlimited number of other genomes in the same view. This allows the biologist to see a gene not just in the context of its genome, but also its regulation and its evolution. Bluejay now has rich provision for personalization by users: (i) numerous display customization features; (ii) the availability of waypoints for marking multiple points of interest on a genome and subsequently utilizing them; and (iii) the ability to take user relevance feedback of annotated genes or textual items to offer personalized recommendations. Bluejay 1.0 also embeds the Seahawk browser for the Moby protocol, enabling users to seamlessly invoke hundreds of Web Services on genomic data of interest without any hard-coding.

Conclusion

Bluejay offers a unique set of customizable genome-browsing features, with the goal of allowing biologists to quickly focus on, analyze, compare, and retrieve related information on the parts of the genomic data they are most interested in. We expect these capabilities of Bluejay to benefit the many biologists who want to answer complex questions using the information available from completely sequenced genomes.

Semi-automatic web service composition for the life sciences using the BioMoby semantic web framework

Researchers in the life-sciences are currently limited to small-scale informatics experiments and analyses because of the lack of interoperability among life-sciences web services. This limitation can be addressed by annotating services and their interfaces with semantic information, so that interoperability problems can be reasoned about programmatically. The Moby semantic web framework is a popular and mature platform that is used for this purpose. However, the number of services that are available to select from when building a workflow is becoming unmanageable for users. As such, attempts have been made to assist with service selection and composition. These tasks fall under the general label of automated service composition. We present a prototype workflow assembly client that reduces the number of choices that users have to make by (1) restricting the overall set of services presented to them and (2) ranking services so that the the most desirable ones are presented first. We demonstrate via an evaluation of this prototype that a unification of relatively simple techniques can rank desirable services highly while maintaining interactive response times.