Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web.

MOTIVATION: High-throughput biological research requires simultaneous visualization as well as analysis of genomic data, e.g. read alignments, variant calls and genomic annotations. Traditionally, such integrative analysis required desktop applications operating on locally stored data. Many current terabyte-size datasets generated by large public consortia projects, however, are already only feasibly stored at specialist genome analysis centers. As even small laboratories can afford very large datasets, local storage and analysis are becoming increasingly limiting, and it is likely that most such datasets will soon be stored remotely, e.g. in the cloud. These developments will require web-based tools that enable users to access, analyze and view vast remotely stored data with a level of sophistication and interactivity that approximates desktop applications. As rapidly dropping cost enables researchers to collect data intended to answer questions in very specialized contexts, developers must also provide software libraries that empower users to implement customized data analyses and data views for their particular application. Such specialized, yet lightweight, applications would empower scientists to better answer specific biological questions than possible with general-purpose genome browsers currently available. RESULTS: Using recent advances in core web technologies (HTML5), we developed Scribl, a flexible genomic visualization library specifically targeting coordinate-based data such as genomic features, DNA sequence and genetic variants. Scribl simplifies the development of sophisticated web-based graphical tools that approach the dynamism and interactivity of desktop applications. AVAILABILITY AND IMPLEMENTATION: Software is freely available online at http://chmille4.github.com/Scribl/ and is implemented in JavaScript with all modern browsers supported.

Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression.

MOTIVATION: A common question arises at the beginning of every experiment where RNA-Seq is used to detect differential gene expression between two conditions: How many reads should we sequence? RESULTS: Scotty is an interactive web-based application that assists biologists to design an experiment with an appropriate sample size and read depth to satisfy the user-defined experimental objectives. This design can be based on data available from either pilot samples or publicly available datasets. AVAILABILITY: Scotty can be freely accessed on the web at http://euler.bc.edu/marthlab/scotty/scotty.php

Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics.

SUMMARY: Biogem provides a software development environment for the Ruby programming language, which encourages community-based software development for bioinformatics while lowering the barrier to entry and encouraging best practices. Biogem, with its targeted modular and decentralized approach, software generator, tools and tight web integration, is an improved general model for scaling up collaborative open source software development in bioinformatics. AVAILABILITY: Biogem and modules are free and are OSS. Biogem runs on all systems that support recent versions of Ruby, including Linux, Mac OS X and Windows. Further information at http://www.biogems.info. A tutorial is available at http://www.biogems.info/howto.html CONTACT: bonnal@ingm.org.

An Sp185/333 gene cluster from the purple sea urchin and putative microsatellite-mediated gene diversification.

BACKGROUND: The immune system of the purple sea urchin, Strongylocentrotus purpuratus, is complex and sophisticated. An important component of sea urchin immunity is the Sp185/333 gene family, which is significantly upregulated in immunologically challenged animals. The Sp185/333 genes are less than 2 kb with two exons and are members of a large diverse family composed of greater than 40 genes. The S. purpuratus genome assembly, however, contains only six Sp185/333 genes. This underrepresentation could be due to the difficulties that large gene families present in shotgun assembly, where multiple similar genes can be collapsed into a single consensus gene. RESULTS: To understand the genomic organization of the Sp185/333 gene family, a BAC insert containing Sp185/333 genes was assembled, with careful attention to avoiding artifacts resulting from collapse or artificial duplication/expansion of very similar genes. Twelve candidate BAC assemblies were generated with varying parameters and the optimal assembly was identified by PCR, restriction digests, and subclone sequencing. The validated assembly contained six Sp185/333 genes that were clustered in a 34 kb region at one end of the BAC with five of the six genes tightly clustered within 20 kb. The Sp185/333 genes in this cluster were no more similar to each other than to previously sequenced Sp185/333 genes isolated from three different animals. This was unexpected given their proximity and putative effects of gene homogenization in closely linked, similar genes. All six genes displayed significant similarity including both 5' and 3' flanking regions, which were bounded by microsatellites. Three of the Sp185/333 genes and their flanking regions were tandemly duplicated such that each repeated segment consisted of a gene plus 0.7 kb 5' and 2.4 kb 3' of the gene (4.5 kb total). Both edges of the segmental duplications were bounded by different microsatellites. CONCLUSIONS: The high sequence similarity of the Sp185/333 genes and flanking regions, suggests that the microsatellites may promote genomic instability and are involved with gene duplication and/or gene conversion and the extraordinary sequence diversity of this family.

SpTie1/2 is expressed in coelomocytes, axial organ and embryos of the sea urchin Strongylocentrotus purpuratus, and is an orthologue of vertebrate Tie1 and Tie2.

A full length cDNA sequence expressed in coelomocytes shows significant sequence match to vertebrate Tie1 and Tie2/TEK. Vertebrate Tie2/TEK is the receptor for the angiopoietins and plays an important role in angiogenesis and hematopoiesis, whereas Tie1 regulates the activity of Tie2. The deduced sequence of the SpTie1/2 protein has a similar order and organization of domains to the homologous vertebrate proteins including a highly conserved receptor tyrosine kinase domain in the cytoplasmic tail. The N terminus of the ectodomain has one immunoglobulin (Ig)-Tie2_1 domain, followed by an Ig domain, four epidermal growth factor domains, a second Ig domain, and three fibronectin type III domains. The SpTie1/2 gene is expressed in coelomocytes and the axial organ, whereas other organs do not show significant expression. The timing of embryonic expression corresponds with the differentiation of blastocoelar cells, the embryonic and larval immune cells. Searches of the sea urchin genome show several gene models encoding putative ligands and signaling proteins that might interact with SpTie1/2. We speculate that SpTie1/2 may be involved in the proliferation of sea urchin immune cells in both adults and embryos.