BOSC 2011: Bioinformatics Open Source Conference, Vienna, Austria, 15-16 July 2011

Bioinformatics Open Source Conference (BOSC) is held annually in conjunction with ISCB's meeting ISMB. BOSC 2011 will be held in conjunction with ISMB/ECCB 2011. BOSC 2011 is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community.

Abstracts for talks and posters are invited for following sessions:

• Approaches to parallel processing.
• Cloud-based approaches to improving software and data accessibility.
• The Semantic Web in open source bioinformatics.
• Data visualization.
• Tools for next-generation sequencing.
• Other Open Source software.

Important Dates:

• April 18, 2011: Deadline for submitting abstracts to BOSC 2011
• May 9, 2011: Notifications of accepted abstracts emailed to corresponding authors
• July 13-14, 2011: Codefest 2011 programming session
• July 15-16, 2011: BOSC 2011
• July 17-19, 2011: ISMB 2011

Web site: http://www.open-bio.org/wiki/BOSC_2011
Email: bosc@open-bio.org

FishBase: A global information system on fishes

FishBase is a relational database with information to cater to different professionals such as research scientists, fisheries managers, zoologists and many more.  FishBase on the web contains practically all fish species known to science. It included descriptions of 31,600 species, 279,100 common names in hundreds of languages, 49,300 pictures, and references to 44,200 works in the scientific literature.

 FishBase was developed at the WorldFish Center in collaboration with the Food and Agriculture Organization of the United Nations ( FAO) and many other partners, and with support from the European Commission ( EC). Since 2001 FishBase is supported by a consortium of nine research institutions. The consortium consists of:

1. World Fish Center
2. Food and Agriculture Organization of the UnitedNations
3. Leibniz-Institut für Meereswissenschaften (IFM)
4. Fisheries Centre University of British Columbia
5. Muséum National d'Histoire Naturelle
6. Royal Museum for Central Africa, Tervuren
7. Chinese Academy of Fishery Sciences
8. Swedish Museum of Natural History
9. Aristotle University of Thessaloniki.

The genetics of koi fish

The commitment of numerous generations of Japanese koi farmers has provided us the modern koi, with its more than 100 types and their distinctive color and pattern variations, some  more desired than others.

The intrinsic qualities of koi, as loved by keepers, breeders and enthusiasts, are governed by a intricate set of genetic and ecological elements.

Modern day koi breeders have broad access to scientific research. The study of genetics in general requires the study of visible characteristics in offspring. Applying conventional techniques, it typically takes 20 generations of devoted, well-planned, selective breeding to be able to establish qualities of preferred character in koi. Results have to be painstakingly recorded and that, unfortunately, is a tradition followed by very few, if any, conventional koi farmers.

Research of koi genetics have been slow, because koi take around two to three years to reach maturity. Carp can mature in a much shorter time, but koi breeders have got inadvertently slowed the rate at which fish achieve maturity even further by breeding for improved body confirmation in order to produce large, show-winning fish. They would never use a female developing gonad at the age of one year.

Recently, advancements in analytical techniques for genome investigation have speeded up genetic research. These techniques were applied into the genetic variability of the koi stock of Niigata’s Yamakoshi region, where a relatively high mortality rate at the larval period had been observed. Koi were obtained from all the significant breeders in the region and examined. The study found that not only was there a low genetic variability inside the Niigata population, but the genetic distance between Kohaku, Sanke and Showa was small, suggesting that these favored kinds originated from a small founding population.

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Electric Eel Genome

Sequencing the complete electric eel genome would be a boon to research on everything from energy production and storage to tissue regeneration, according to some scientists.

Six American researchers wrote a review, published  in the Journal of Fish Biology, calling for dense, seven- to 11-fold shotgun sequencing of the electric eel genome - a move they said would provide information about more than 95 percent of the fish’s genome as well as its genetic scaffold.

Electric eels, Electrophorus electricus, can generate bioelectricity from chemical food energy using specialized electric organs. These contain electrically-charged cells that, in turn, house precisely regulated ion channels and receptors. Together, this system lets electric eels generate electrical pulses ranging from weak, millivolt discharges to strong zaps up to 600 volts.

Another advantage to this particular creature is its ability to regenerate some tissues and organs - including its spinal chord - after injury. Peeking into the eel’s genome may explain this, as well as its complex evolution and neurophysiology.

Workshop on Molecular Evolution: North America, 24 July - 6 August 2011

The Workshop on Molecular Evolution consists of a series of lectures, demonstrations and computer laboratories that cover various aspects of molecular evolution. Demonstrations and consultations on the use of computer programs and packages such as BLAST, BEAST, Clustal W and Clustal X, FASTA, FigTree, GARLI, Genealogical Sorting Index, LAMARC, MAFFT, Migrate-n, MrBayes, PAML, PAUP*, and SeaView will be provided. The course is designed for established investigators, postdoctoral scholars, and advanced graduate students with prior experience in molecular evolution and related fields. Admission is limited and highly competitive, with admissions decisions determined by an international committee.

Topics to be covered include:

• Databases and sequence matching: database searching: protein sequence versus protein structure; homology; mathematical, statistical, and theoretical aspects of sequence database searches
• Phylogenetic analysis: theoretical, mathematical and statistical bases; sampling properties of sequence data; Bayesian analysis; hypothesis testing
• Maximum likelihood theory and practice in phylogenetics and population genetics: coalescent theory; maximum likelihood estimation of population genetic parameters
• Molecular evolution integrated at organism and higher levels: population biology; biogeography; ecology; systematics and conservation
• Molecular evolution and development: gene duplication and divergence; gene family organization; coordinated expression in evolution
• Comparative genomics: genome content; genome structure; genome evolution
• Molecular evolution integrated at lower levels: biochemistry; cell biology; physiology; relationship of genotype to phenotype

Venue: Colorado State University, Fort Collins, Colorado, USA

Application form and complete schedule are available online.

Coding sequence evolution in salmonids

The combination of next generation sequencing with a comparative genomics approach appears particularly promising towards yielding detailed insights into issues related to evolutionary biology. Very recently canadian scientists applied this strategy to investigate patterns of nucleotide substitutions in five species of the salmonid family (Salmo salar, Onchorynchus mykiss, Salvelinus fontinalis, Salvelinus namaycush, Coregonus clupeaformis) and compare this information with other fishes (Esox lucius, Danio rerio) for which genome information is available in order to infer the role of natural selection on the evolution of protein coding genes.

Results of the study warrant further investigation in regards to the putative role of positive selection in the process of adaptive divergence in salmonids. Findings of this study are published in the latest issue of Molecular Biology and Evolution.

NGSmethDB: Database for next-generation sequencing whole genome methylation

Next-generation sequencing (NGS) together with bisulphite conversion allows the generation of whole genome methylation maps at single-cytosine resolution. This allows studying the absence of methylation in a particular genome region over a range of tissues, the differential tissue methylation or the changes occurring along pathological conditions. The first database NGSmethDB proposed by Spanish scientists fully address such requirements for the storage and retrieval of methylation data derived from NGS (published in Molecular biology and Evolution) . The database uses a web interface based on GBrowse and coupled to a MySQL backend, which allows to visualize the methylation data in a genomic context together with many other annotations, as well as full data downloads.

Basic features of the database:

1. Two different cytosine methylation contexts are considered. First, the CpG dinucleotides and second the CAG/CTG pattern, which have been shown recently to be able to methylate in undifferentiated cells.
2. The user can search for all methylation contexts which are unmethylated or differentially methylated in a given set of tissues.
3. The user can retrieve all methylation values for a given set of tissues in a given chromosomal region.
4. The database allows displaying the methylation among different tissues in the promoter regions of RefSeq genes.
5. Methylation values can be retrieved for a given chromosomal region.
6. Dump downloads exist for two different read coverage: methylation contexts covered by at least 1 read, and those covered by at least 10 reads.

NGSmethDB will be useful for experimental researchers, as well as for bioinformaticians, who might use the data as input for further research.

Workshop on Comparative Genomics: North America, 10-23 July, 2011

The Workshop on Comparative Genomics will consist of a series of lectures, demonstrations and computer laboratories that cover various aspects of comparative genomics. The course is designed for established investigators, postdoctoral scholars, and advanced graduate students. Admission is limited and highly competitive, with admissions decisions determined by an international committee.

Topics to be covered include:

• Sequencing technologies: short-read sequencing technologies of various types
• Assembly and alignment: basic analyses in de novo and resequencing studies
• Gene finding and annotation: functional description of genomic data
• Genome characterization: gene content; genome structure; synteny; SNPs; copy number variation (CNV)
• Assigning sequences to taxonomic groups in metagenomic studies: moving from sequences of unknown taxa to known taxa

Venue: Colorado State University, Fort Collins, Colorado, USA

Application forms and complete schedule are available online.

cBARBEL: Catfish Breader And Researcher Bioinformatics Entry Location

cBARBEL is an online open-access database for genome biology of Ictalurus spp.. It is a comprehensive, integrative platform for all aspects of catfish genetics, genomics and related data resources. cBARBEL provides BLAST-based, fuzzy and specific search functions, visualization of catfish linkage, physical and integrated maps, a catfish EST contig viewer with SNP information overlay, and GBrowse-based organization of catfish genomic data based on sequence similarity with zebrafish chromosomes. 

cBARBEL provides links to simple daily-use informatics tools that database users may need while accessing cBARBEL, including the external NCBI BLAST server, SMART domain search, ClustalW-based multiple sequence alignments and basic nucleotide to amino acid translation. These tools are provided in-frame so that the user does not need to leave the cBARBEL site for small-scale sequence analysis. Publications relevant to catfish genomics and genetics are also linked. Additionally, the recently created Teleost Alternative Splicing Database (TASD) with alternative splicing data for catfish ESTs is linked to cBARBEL.

TASD: Teleost Alternative Splicing Database

Alternative splicing  (AS) is recognized as one of the mechanisms by which the coding capacity and diversity of the genome can be amplified. Scientists have recently conducted the first major genome-wide analysis of AS in teleost fish. An online database  for teleost AS was created using the ASviewer format.  The database (TASD) is publically available and allows easy identification and visualization of AS transcripts in the teleost genomes.

Users of the database can search for the number, type, and location of AS genes in channel catfish, fugu, medaka, zebrafish, and stickleback as well as visualizing the AS event. AS information will be added for additional species as warranted.

Salmon louse: Gene expression analysis of immune response during infection

The salmon louse (Lepeophtheirus salmonis kroyer) an ectoparasitic copepod causes significant loss in salmon aquaculture. Recently scientist have used 21 k oligonucleotide microarray and RT-qPCR to examine the time course of immune gene expression changes in salmon skin, spleen and head kidney during challenge of copepod and chalimus stages of lice development.

Rapid sensing was witnessed with induction of genes involved in innate immunity in skin and spleen. Transient increase in T-cell receptor alpha, CD4-1, and possible regulators of lymphocyte differentiation suggests recruitment of T-cells to the skin. Up regulation of putative lymphocyte G0/G1 switch proteins in spleen, immunoglobulins and increase of IgM and IgT transcripts in skin indicated a transition from innate to adaptive humoral immune response.

Results are published in latest issue of BMC Genomics.

Tetraodon genome project

The Tetraodon genome project is a collaboration between Genoscope and the Broad Institute (MIT). This Ensembl website presents sequence data and analyses provided by the two institutes.

The project was supported by the Consortium National de Recherche en Genomique and the National Human Genome Research Institute.

Genes were annotated by Genoscope, combining evidence from Geneid, Genscan, Genewise and Exofish predictions with alignments of Tetraodon cDNAs to the genome. The annotation also includes 87 manually curated structures of a number of HOX and Cytokine genes.

ICSASG: International Collaboration to Sequence Atlantic Salmon Genome

ICSASG will produce a genome sequence that identifies and physically maps all genes in the Atlantic salmon genome and acts as a reference sequence for other salmonids. The ICSASG has raised sufficient funds to cover the cost of sequencing, assembling and annotating the Atlantic salmon genome. It is anticipated that when the sequence becomes available, other opportunities will arise and the framework established by the ICSASG can be expanded to encompass projects such as sequencing other salmonid genomes using the Atlantic salmon as a reference sequence. A website Consortium for Genomic Research on All Salmonids Program [C GRASP] was set up as a portal for other websites that host salmonid genomic data, as well as providing information concerning on-going projects, collaborative opportunities and contact information for the ICSASG.

Nile Tilapia: Whole genome sequencing

Non-mammalian animals can provide great insight into the principles of development and evolution, which in turn teaches us about human biology and disease. The Broad Institute is generating a high quality draft from a Nile tilapia, Oreochromis niloticus. The Nile tilapia is 10-15 million years diverged from the East African lake cichlids, and provides a good outgroup for the study of the remarkable speciation among the cichlids in those lakes. In addition, the Broad is producing high quality drafts of 4 additional cichlid species representing a broad cross-section of the East African Lake lineages:  Astatotilapia burtoni, Malawi (Maylandia) zebra, Pundamila nyererei and Neolamprologus brichardi. 

A large number of BAC end sequences (110,880) have been generated at Genoscope. The BAC end sequences have been comparatively mapped in silico by Kocher's lab to stickleback genome sequence assembly. Working with Co-Factor Genomics, Kocher's lab is also generating the whole genome sequences of the tilapia genome using the next generation sequencing. A total of 116,889 ESTs have been generated in Kocher's lab from 17 normalized libraries. These ESTs were assembled into 24,363 contigs

These genomic resources will not only help researchers address important questions about vertebrate evolution, but will also enable the study of behavior, immunology, and toxicology. They will also contribute to the maintenance and improvement of the tilapia as an important food source in over 100 countries and one of the primary sources of protein in the developing world.