BRAT: bisulfite-treated reads analysis tool

BRAT is a new, accurate and efficient tool for mapping short reads obtained from the Illumina Genome Analyzer following sodium bisulfite conversion. BRAT, supports single and paired-end reads and handles input files containing reads and mates of different lengths. BRAT is faster, maps more unique paired-end reads and has higher accuracy than existing programs. The software package includes tools to end-trim low-quality bases of the reads and to report nucleotide counts for mapped reads on the reference genome.

Availability: The source code is freely available for download at http://compbio.cs.ucr.edu/brat/ and is distributed as Open Source software under the GPLv3.0.

MARTA: A suite of Java-based tools for assigning taxonomic status to DNA sequences

A suite of Java-based software has been created to better provide taxonomic assignments to DNA sequences. It's anticipated that the program will be useful for protistologists, virologists, mycologists and other microbial ecologists. The program relies on NCBI utilities including the BLAST software and Taxonomy database and is easily manipulated at the command-line to specify a BLAST candidate's query-coverage or percent identity requirements; other options include the ability to set minimal consensus requirements (%) for each of the eight major taxonomic ranks (Domain, Kingdom, Phylum, ...) and whether to consider lower scoring candidates when the top-hit lacks taxonomic classification.

Availability: http://bergelson.uchicago.edu/software/marta

Bisque: a platform for bioimage analysis and management

Advances in the field of microscopy have brought about the need for better image management and analysis solutions. Novel imaging techniques have created vast stores of images and metadata that are difficult to organize, search, process and analyze. These tasks are further complicated by conflicting and proprietary image and metadata formats, that impede analyzing and sharing of images and any associated data. These obstacles have resulted in research resources being locked away in digital media and file cabinets. Current image management systems do not address the pressing needs of researchers who must quantify image data on a regular basis.
Results: We present Bisque, a web-based platform specifically designed to provide researchers with organizational and quantitative analysis tools for 5D image data. Users can extend Bisque with both data model and analysis extensions in order to adapt the system to local needs. Bisque's extensibility stems from two core concepts: flexible metadata facility and an open web-based architecture. Together these empower researchers to create, develop and share novel bioimage analyses. Several case studies using Bisque with specific applications are presented as an indication of how users can expect to extend Bisque for their own purposes.
Availability: Bisque is web based, cross-platform and open source. The system is also available as software-as-a-service through the Center of Bioimage Informatics at UCSB.

Beta Glucan MH3 - Immune System Video

Beta-glucans are known as "biological response modifiers" because of their ability to activate the immune system.Immunologists at the University of Louisville, discovered that a receptor on the surface of innate immune cells called Complement Receptor 3 (CR3 or CD11b/CD18) is responsible for binding to beta-glucans, allowing the immune cells to recognize them as "non-self." However, it should be noted that the activity of beta-glucans is different from some pharmaceutical drugs which have the ability to over-stimulate the immune system. Pharmaceutical drugs have the potential to push the immune system to over-stimulation, and hence are contraindicated in individuals with autoimmune diseases, allergies, or yeast infections. Beta-glucans seem to make the immune system work better without becoming overactive. In addition to enhancing the activity of the immune system, beta-glucans also reportedly lower elevated levels of LDL cholesterol, aid in wound healing, help prevent infections, and have potential as an adjuvant in the treatment of cancer.

http://www.biosolutions.info/2010/02/beta-glucan-mh3-immune-system-video.html