Biopipe: A Flexible Framework for Protocol-Based Bioinformatics Analysis

Hoon, Shawn; Ratnapu, Kiran Kumar; Chia, Jer Ming; Kumarasamy, Balamurugan; Juguang, Xiao; Clamp, Michele; Stabenau, Arne; Potter, Simon; Clarke, Laura; Stupka, Elia

doi:10.1101/gr.1363103

Cited by 72 publications

(43 citation statements)

References 18 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The structured storage and reusability of generated results is a critical point for the protocol based step by step modeling of more complex experiments/workflows [15]. In Genlight the re-use of derived results is a central concept.…”

Section: System Architecturementioning

confidence: 99%

Genlight: Interactive high-throughput sequence analysis and comparative genomics

Beckstette¹,

Mailänder²,

Marhöfer³

et al. 2004

Journal of Integrative Bioinformatics

View full text Add to dashboard Cite

With rising numbers of fully sequenced genomes the importance of comparative genomics is constantly increasing. Although several software systems for genome comparison analyses do exist, their functionality and flexibility is still limited, compared to the manifold possible applications. Therefore, we developed Genlight, a Client/Server based program suite for large scale sequence analysis and comparative genomics. Genlight uses the object relational database system PostgreSQL together with a state of the art data representation and a distributed execution approach for large scale analysis tasks. The system includes a wide variety of comparison and sequence manipulation methods and supports the management of nucleotide sequences as well as protein sequences. The comparison methods are complemented by a large variety of visualization methods for the assessment of the generated results. In order to demonstrate the suitability of the system for the treatment of biological questions, Genlight was used to identify potential drug and vaccine targets of the pathogen Helicobacter pylori.Availability: The Genlight system is publicly available for non-commercial use on

show abstract

Section: System Architecturementioning

confidence: 99%

Genlight: Interactive high-throughput sequence analysis and comparative genomics

Beckstette¹,

Mailänder²,

Marhöfer³

et al. 2004

Journal of Integrative Bioinformatics

View full text Add to dashboard Cite

show abstract

“…Their contribution has been to allow data and analysis tools to be seen as interacting components (e.g., Intelli-GEN [9]). A more recent initiative is Biopipe [5]. The design of ISXL assumes that all the above proposals are meritorious in their goal.…”

Section: Related Workmentioning

confidence: 99%

A LANGUAGE-BASED APPROACH FOR COMPREHENSIVELY SUPPORTING THEIN SILICOEXPERIMENTAL PROCESS

Tröger

Fernandes

2005

Int. J. Soft. Eng. Knowl. Eng.

View full text Add to dashboard Cite

One of the challenges for bioinformaticians is to approximate, in silico, tried and tested research methods used in vitro. One of the problems standing in their way is the lack of a concrete framework for designing and expressing in silico experiments that aim at being isomorphic to in vitro experiments. This paper introduces such a framework in the form of a specification language called ISXL. ISXL projects to biologists a model of in silico experiments that approximates the research method they are most familiar with, as follows. An ISXL-specified experiment (1) conforms to a conceptual model that explicitly captures the basic constituents of experiments in the empirical sciences; (2) may be defined in relation to explicit hypothesis formulation and validation rather than simply taking the form of an evidence gathering process as in alternative approaches; (3) may be long-lived and evolve over time, in the sense that there is built-in support for denoting past versions of specifications, past results, past hypotheses, past validation criteria; (4) may denote other experiments and their constituent parts, thereby reflecting the interrelatedness of scientific processes. Features (1)-(4) above are made possible by endowing ISXL with certain characteristics of a persistent workflow environment. This allows ISXL experiments to be rich in metadata without imposing too great a burden on the biologist. The metadata in turn open the way for ISXL experiments to be capable of introspection and reflection. This paper focuses on describing of ISXL conceptually and syntactically, and indicates how ISXL experiments are given a formal semantics.

show abstract

“…Some of them are add-ons to other tools, like biopipe [15], a perl module designed to be used with bioperl, and GPipe, an extension of the Pise interface [16]. Other systems are autonomous applications that are being developed either by industries, like the Bioinformatic Workflow Builder Interface -BioWBI from IBM [17], and Pipeline Pilot from SciTegic, or by academic and research institutes, like Wildfire from the Singapore Bioinformatics Institute, and Taverna Workbench [18] from the European Bioinformatics Institute (EBI).…”

Section: Introductionmentioning

confidence: 99%

Network integration of data and analysis of oncology interest

Romano¹,

Bertolini

Paoli

et al. 2006

Journal of Integrative Bioinformatics

View full text Add to dashboard Cite

SummaryThe Human Genome Project has deeply transformed biology and the field has since then expanded to the management, processing, analysis and visualization of large quantities of data from genomics, proteomics, medicinal chemistry and drug screening. This huge amount of data and the heterogeneity of software tools that are used implies the adoption on a very large scale of new, flexible tools that can enable researchers to integrate data and analysis on the network. ICT technology standards and tools, like Web Services and related languages, and workflow management systems, can support the creation and deployment of such systems. While a number of Web Services are appearing and personal workflow management systems are also being more and more offered to researchers, a reference portal enabling the vast majority of unskilled researchers to take profit from these new technologies is still lacking. In this paper, we introduce the rationale for the creation of such a portal and present the architecture and some preliminary results for the development of a portal for the enactment of workflows of interest in oncology.

show abstract

Biopipe: A Flexible Framework for Protocol-Based Bioinformatics Analysis

Cited by 72 publications

References 18 publications

Genlight: Interactive high-throughput sequence analysis and comparative genomics

Genlight: Interactive high-throughput sequence analysis and comparative genomics

A LANGUAGE-BASED APPROACH FOR COMPREHENSIVELY SUPPORTING THEIN SILICOEXPERIMENTAL PROCESS

Network integration of data and analysis of oncology interest

Contact Info

Product

Resources

About