Software Development

BGI Cloud Computing project aims at creating a software environment enabling users to make a large number of bioinformatics analyses, combined with smooth data management and excellent graphical viewing and output options. Our team puts efforts mainly on integrating self-developed powerful tools and efficient workflows of bioinformatics research, especially focusing tools optimized for the analysis of nucleotide sequences from next generation sequencing technology into BGI Cloud Computing with friendly user interface,  such as short oligo nucleotide alignment program (SOAP), De novo assembly tools et. This bioinformatics platform will enable both private and public research and implement the new sequencing technologies quicker, reap the benefits faster.

Ongoing projects:

We are now focusing on introducing Solexa sequencing analysis service as below:

1. Tag-based mRNA profiling is a revolutionary approach for expression analysis that generates expression profiles for any transcript from any organism. Driven by Solexa Sequencing, tag-based mRNA profiling creates whole genome wide expression profiles by sequencing over 1 million cDNA tags per sample rather than employing hybridization techniques such as gene expression microarrays. We have developed a pipeline to analysis the sequencing data of this solution, which finally generate an expert report.

2. MIREAP is a program that identifies both known and novel miRNAs from deep sequenced small RNA libraries with additional criteria. We use a methodology including full consideration of miRNA biogenesis, sequencing depth, and structural features to improve the sensitivity and specificity of miRNA identification.

Database

This is one of the most productive group majoring on database construction and web-based applications development. To make better understanding and availability of the massive data BGI generated, we set up sites for project introduction, genome browsing, data downloading and related issues. We also provide services on traditional genome analysis and accessing of relevant tools. Concerned databases and services can be accessed at http://bioinformatics.genomics.org.cn/bio/databases.html

 Ongoing Projects:

1) YH database http://yh.genomics.org.cn/index.jsp

BGI finished sequencing the first diploid Asian human genome and we are setting up the database and web site. It is composed of a blast service, a Gbrowse-based genome viewer and YH genotype/phenotype search engine. The map viewer can unprecedentedly exhibit all short reads alignments which makes variants markedly distinguishable. And this site is also a primitive attempt to personal medicine.

One can view and access YH data including raw sequences, alignments, consensus genome and variants against NCBI Human v36.

2) Silkworm polymorphism database

Tens of silkworms are being sequenced and a study on polymorphism map is ongoing. A database and web site will be establish for viewing silkworm genome and polymorphism. Online mapping and phylogeny analysis will too be provided soon.

3) Generic genome database platform

New sequencing technology brings out an era of new species genome sequencing. We decided to develop a platform to contain all genomes we have done and we are going to sequence.

 IT & System support

Our mission is to provide the best services and technical support including data management and system maintenance for our scientists and any BLC (Bioinformatics Linux Cluster) user and to further contribute to support their highest demands in BLC by investigating and testing cutting-edge computer technology.

Responsibility:

1. Data management(upload, download and backup), Web/Database server admin, and Electronic documents management.

2. Design, maintain, and implement BLC cluster and infrastructure servers.

3. Providing assistance with software installation and troubleshooting to system users.

4. Implementing and helping to evaluate new technologies in fields such as parallel file systems, high-speed interconnects, and parallel computing architectures.