Bioinformatics Tool-Related Papers of Note, February 2010
Babur O, Dogrusoz U, Demir E, Sander C. ChiBE: interactive visualization and manipulation of BioPAX pathway models. [Bioinformatics. 2010 Feb 1;26(3):429-31]: Describes ChiBE, open source software that features display, navigation, and manipulation of pathway models in BioPAX format. Pathway views can be laid out and edited with a number of visualization methods, including compound or nested structures for visualizing cellular compartments and molecular complexes. Available here.
Brooijmans N, Chang YW, Mobilio D, Denny RA, Humblet C. An enriched structural kinase database to enable kinome-wide structure-based analyses and drug discovery. [Protein Sci. 2010 Feb 4 (e-pub ahead of print)]: Discusses a kinase structural database called the Kinase Knowledge Base, or KKB. The database covers all human kinase domain structures that have been deposited in the Protein Data Bank, according to the paper's abstract. All structures are renumbered using a common scheme that enables "efficient cross-comparisons and multiple queries of interest to the kinase field." This numbering scheme is also used to automatically annotate conserved residues and motifs, and conformationally classify the structures based on the DFG-loop and helix C.
Cerami E, Demir E, Schultz N, Taylor BS, Sander C. Automated network analysis identifies core pathways in glioblastoma. [PLoS One. 2010 Feb 12;5(2):e8918]: Proposes an automated network-based approach for identifying candidate oncogenic processes and driver genes that is based on the hypothesis that cellular networks contain functional modules, and that tumors target specific modules critical to their growth. The approach combines analysis of sequence mutations and DNA copy number alterations, a unified molecular interaction network that includes both protein-protein interactions and signaling pathways, and identification and statistical assessment of network modules, which the authors define as "cohesive groups of genes of interest with a higher density of interactions within groups than between groups." The approach, implemented in a software package called NetBox, is available here.
Cooling MT, Rouilly V, Misirli G, Lawson J, Yu T, Hallinan J, Wipat A. Standard virtual biological parts: A repository of modular modeling components for synthetic biology. [Bioinformatics. 2010 Feb 16 (e-pub ahead of print)]: Introduces an online repository that includes a collection of standardized models "that can readily be recombined to model different biological systems using the inherent modularity support of the CellML 1.1 model exchange format," the paper's abstract states. Available here.
Dada JO, Spasic I, Paton NW, Mendes P. SBRML: a markup language for associating systems biology data with models. [Bioinformatics. 2010 Feb 21 (e-pub ahead of print)]: Describes the Systems Biology Results Markup Language, or SBRML, an XML-based language that associates a model with several data sets. "Each data set is represented as a series of values associated with model variables, and their corresponding parameter values," the paper's abstract states. While there are a number of data standards for systems biology research, including SBML, FuGE, and the Proteomics Standards Initiative, "until now, there has been no standard way to associate a model and its entities to the corresponding data sets, or vice versa," the authors note. SBRML "provides a flexible way of indexing the results to model parameter values, which supports both spreadsheet-like data and multidimensional data cubes." Available here.
Jiang P, Singh M. SPICi: a fast clustering algorithm for large biological networks. [Bioinformatics. 2010 Feb 24. (e-pub ahead of print)]: Introduces a fast local network clustering algorithm called SPICi that is "typically several orders of magnitude faster than previous approaches and is the only one that can successfully cluster all test networks within very short time," according to the paper's abstract. Available here.
Kvilekval K, Fedorov D, Obara B, Singh A, Manjunath BS. Bisque: A platform for bioimage analysis and management. [Bioinformatics. 2010 Feb 15;26(4):544-52]: Describes Bisque, a web-based platform containing organizational and quantitative analysis tools for 5D image data. Users can deploy both data model and analysis extensions "in order to adapt the system to local needs," the paper's abstract states. Bisque offers a flexible metadata facility and an open web-based architecture that together "empower researchers to create, develop, and share novel bioimage analyses." Available here.
Lefever S, Hoebeeck J, Pattyn F, Tusnády G, De Paepe A, Speleman F, Arányi T, Vandesompele J. methGraph: A genome visualization tool for PCR-based methylation assays. [Epigenetics. 2010 Feb 11;5(2)]: Discusses methGraph, a web application for visualizing and evaluating PCR-based methylation assays. Researchers can use the BiSearch ePCR algorithm to submit PCR primer sequences for specificity assessment and mapping on the genome, then select relevant UCSC genome annotation tracks for display in the final graph. The software provides a custom track that shows all individual CpG dinucleotides and represents their distribution in the CpG island. Available here.
Milne I, Bayer M, Cardle L, Shaw P, Stephen G, Wright F, Marshall D. Tablet — next generation sequence assembly visualization. [Bioinformatics. 2010 Feb 1;26(3):401-2]: Presents Tablet, a graphical viewer for next-generation sequence assemblies and alignments that supports a range of input assembly formats. Tablet "provides high-quality visualizations showing data in packed or stacked views, allowing instant access and navigation to any region of interest, and whole contig overviews and data summaries," according to the paper's abstract. Available here.
Parks DH, Beiko RG. Identifying biologically relevant differences between metagenomic communities. [Bioinformatics. 2010 Mar 15;26(6):715-21]: Introduces STAMP, a software package for comparative metagenomics that supports "best practices in analysis and reporting," according to the paper's abstract. Available here.
Sartor MA, Mahavisno V, Keshamouni VG, et al. ConceptGen: a gene set enrichment and gene set relation mapping tool. [Bioinformatics 2010 Feb 15;26(4):456-63]: Describes ConceptGen, a web-based gene set enrichment and gene set relation mapping tool that offers more than 20,000 concepts. These concepts comprise "fourteen different types of biological knowledge, including data not currently available in any other gene set enrichment or gene set relation mapping tool," according to the paper's abstract. Available here.
Stacy Duncan , Ruchita Sirkanungo , Leslie Miller and Gregory J Phillips DraGnET: Software for storing, managing, and analyzing annotated draft genome sequence data. [BMC Bioinformatics 2010 Feb 22;11(1):100]: Presents DraGnET (Draft Genome Evaluation Tool), an open source web application that allows researchers without programming experience to set up in-house projects for storing, retrieving, organizing, and managing annotated draft and complete genome sequence data. The software provides a web interface for Blast that allows users to perform preliminary comparative analysis among multiple genomes. Available here.