MOWSERV 2: Friendly and extensible web platform for bioinformatics tools integration (original) (raw)

MOWServ: a web client for integration of bioinformatic resources

Nucleic Acids Research, 2010

The productivity of any scientist is affected by cumbersome, tedious and time-consuming tasks that try to make the heterogeneous web services compatible so that they can be useful in their research. MOWServ, the bioinformatic platform offered by the Spanish National Institute of Bioinformatics, was released to provide integrated access to databases and analytical tools. Since its release, the number of available services has grown dramatically, and it has become one of the main contributors of registered services in the EMBRACE Biocatalogue. The ontology that enables most of the web-service compatibility has been curated, improved and extended. The service discovery has been greatly enhanced by Magallanes software and biodataSF. User data are securely stored on the main server by an authentication protocol that enables the monitoring of current or already-finished user's tasks, as well as the pipelining of successive data processing services. The BioMoby standard has been greatly extended with the new features included in the MOWServ, such as management of additional information (metadata such as extended descriptions, keywords and datafile examples), a qualified registry, error handling, asynchronous services and service replication. All of them have increased the MOWServ service quality, usability and robustness. MOWServ is

Software tools in Bioinformatics: A survey on the importance and Issues faced in implementation

Bioinformatics tools are very complex and critical software tools in life sciences. Bioinformatics tools in today’s world range from simple basic tools to very large sophisticated software packages. In spite of increasing complexity and sophistication of the bioinformatics tools, these tools are increasingly used in the field of modern biology. This introduction of software tools in the field of modern biology has its distinct advantages as well as there are some challenges in their implementation. This study was conducted in keeping with the aim of discussing these advantages and challenges faced with the implementation of bioinformatics tools. This paper has two main objectives; first discusses the challenges faced in the development of bioinformatics tools from a software development point of view. Second, the results of the survey based on the importance and issues in bioinformatics tools are presented from an end user point of view. The main audience of this survey were student...

A web services based framework for uniform integration of command-line bioinformatics software tools

Innovations in Information …

 Abstract-Life scientists use a variety of bioinformatics software tools to perform tasks such as annotation of DNA and protein sequences. Most of these tools are command-line driven and handle various data types (nucleotide, protein, etc.) and data formats (Fasta, Genbank, GCG, etc.). As many bioinformatics software tools are generally involved in analysis tasks, scientists are more and more requiring that these heterogeneous bioinformatics tools be integrated in a uniform way. They are also requiring graphical user interfaces of these tools, and the ability to compose workflows without much programming effort. In this paper, we propose a Web services based framework that meets the above requirements.

An integration platform for heterogeneous bioinformatics software components

2001

Abstract Although computer programs and database resources for bioinformatics applications are becoming more widely available, these resources are unstandardized and frequently incompatible. The problem of integrating heterogeneous software is of immense importance to the field, especially because a rapid pace of change and a general scarcity of development resources discourage re-engineering and compel developers to find ways to use legacy resources.

The Gaggle: An open-source software system for integrating bioinformatics software and data sources

BMC Bioinformatics, 2006

Background: Systems biologists work with many kinds of data, from many different sources, using a variety of software tools. Each of these tools typically excels at one type of analysis, such as of microarrays, of metabolic networks and of predicted protein structure. A crucial challenge is to combine the capabilities of these (and other forthcoming) data resources and tools to create a data exploration and analysis environment that does justice to the variety and complexity of systems biology data sets. A solution to this problem should recognize that data types, formats and software in this high throughput age of biology are constantly changing.

MAPI: Towards the integrated exploitation of bioinformatics Web Services

BMC Bioinformatics, 2011

Background: Bioinformatics is commonly featured as a well assorted list of available web resources. Although diversity of services is positive in general, the proliferation of tools, their dispersion and heterogeneity complicate the integrated exploitation of such data processing capacity.

Open source tools and toolkits for bioinformatics: significance, and where are we

Briefings in Bioinformatics, 2006

This review summarizes important work in open-source bioinformatics software that has occurred over the past couple of years. The survey is intended to illustrate how programs and toolkits whose source code has been developed or released under an Open Source license have changed informatics-heavy areas of life science research. Rather than creating a comprehensive list of all tools developed over the last 2^3 years, we use a few selected projects encompassing toolkit libraries, analysis tools, data analysis environments and interoperability standards to show how freely available and modifiable open-source software can serve as the foundation for building important applications, analysis workflows and resources.

The EMBL-EBI bioinformatics web and programmatic tools framework

Nucleic acids research, 2015

Since 2009 the EMBL-EBI Job Dispatcher framework has provided free access to a range of mainstream sequence analysis applications. These include sequence similarity search services (https://www.ebi.ac.uk/Tools/sss/) such as BLAST, FASTA and PSI-Search, multiple sequence alignment tools (https://www.ebi.ac.uk/Tools/msa/) such as Clustal Omega, MAFFT and T-Coffee, and other sequence analysis tools (https://www.ebi.ac.uk/Tools/pfa/) such as InterProScan. Through these services users can search mainstream sequence databases such as ENA, UniProt and Ensembl Genomes, utilising a uniform web interface or systematically through Web Services interfaces (https://www.ebi.ac.uk/Tools/webservices/) using common programming languages, and obtain enriched results with novel visualisations. Integration with EBI Search (https://www.ebi.ac.uk/ebisearch/) and the dbfetch retrieval service (https://www.ebi.ac.uk/Tools/dbfetch/) further expands the usefulness of the framework. New tools and updates such...