上海生命科学研究院生物信息学中心简介

    生物信息学中心成立于2000年六月，作为上海生命科学研究院内的重要支撑平台之一，中心主任为李亦学研究员。生物信息学中心的一个重要的工作是：面向生科院内部的课题组，根据相关的需求开展生物信息学的支撑工作，包括为生科院内外各课题组提供生物信息学相关的咨询服务，帮助他们运用生物信息学的工具和方法来查询，分析有关的实验信息；根据有关研究组，中心等的实际需求来帮助其开发生物信息学应用系统和软件；及时地将有关的新方法，系统介绍进来，开办各种生物信息学培训班，向广大生物学工作人员介绍新的生物信息学知识,研究方法和手段以及软件和系统的使用。

    同时，中心的另一个任务是面向生物学上的热点及关键问题，开展相关的生物信息学的研究工作。目前，一共有3个课题组，分工如下：

    结构基因组信息分析课题组：蛋白质组学中的生物信息学研究；蛋白质－蛋白质相互作用网络分析、蛋白质结构与功能分析预测、基于基因组信息的药物作用靶标发现与确证。

    生物信息技术研发与服务课题组：负责生物信息数据库建设，实验室信息管理系统设计和开发，生物信息学分析软件开发、安装、升级和维护，生科院内外的生物信息学技术服务和技术支撑。

    功能基因组信息分析课题组：基因组信息整合与分析，比较基因组研究、基因表达谱和基因调控网络分析。

中心人员组成：

    由二部分组成：受聘用的工作人员和研究生。目前，工作人员共有14人,其中高级科研人员4名，中级科研人员5名；博士生16名，硕士生4名，其中在职硕士生1名，各类具有生物和计算机背景的软件编程人员11人。已经形成了一支初具规模，具有较高水平生物信息学研究和实践经验的研发队伍。

    作为中科院上海生命科学研究院的主要生物技术支撑平台，本中心在重大科研发展领域担负着许多重大课题和服务项目。其中有：国家重大专项――国际人类肝脏蛋白质组学的生物信息学课题，多项国家973、863、中科院、上海市生物技术领域的重大、重点课题，同时与生科院外的多家院所合作开展生物信息学研究，其中包括人类基因组国家南方中心、上海第二医科大学、上海交通大学、上海芯片公司、上海大学等，承担了多种合作科研项目。生物信息中心已开发和在建的数据库有：蛋白质功能注释系统、核酸序列数据库、生物芯片数据库、蛋白质组学数据库、人类单核苷酸多态性数据库、中国基因研究统计数据库、跨膜蛋白专门数据库、电子克隆专家系统系、蛋白质跨膜区拓扑结构预测的生物信息学分析软件。EMBL的集成化的数据库检索系统SRS软件包已顺利安装在中心的服务器上，所附带的一百多个国际著名公开数据库，如EMBL、NCBI、Swiss-Prot等已经实现日更新。因此，在数据库的开发和管理上已积累了相当的经验。本中心还参与了水稻基因组，钩端螺旋体基因组的研究工作，有关水稻基因组的成果已经发表在<Science>杂志上，钩端螺旋体基因组的研究成果发表在<Nature>杂志上，钩端螺旋体蛋白质组的研究也积累了大量的数据。作为发表在<Science>上SARS病毒分子流行病学研究的共同第一作者参与了大量的抗SARS的研究工作。中心的网站：www.biosino.org已成为国内生物信息学领域最有影响的专业网站之一。

科研条件：

    中国科学院上海生命科学研究院生物信息中心目前已有SGI Altix350, 1.4GHz 32CPU 大型机一台, 128GB内存，6T磁盘阵列；SGI Origin 2000 8CPU的大型机一台，8G内存，720G硬盘, Dell PowerEdge 1750 服务器一台，3.2GHz 10CPUs, 10G 内存, 750G 硬盘; 神威 新世纪服务器一台，双CPU 18节点, 680G硬盘, SGI O2 工作站3台，Blast、phrap并行化的软件已经于2000年11月底通过调试安装在中心的这台SGI大型机上。目前，安装在中心的SGI大型机上的高可用性的Blast软件HP-Blast 相对运算速度具国内首位。各类单、双CPU PC服务器40余台，四节点、8CPU SGI PC-Cluster一台，16节点32CPU的SW-Cluster一台，峰值运算速度达到270亿/秒，主要用于运行自主开发的并行化和高可用性和高速的SW-Blast软件。基础设施投入已达600多万人民币，结合SGI开发的并行优化的Blast、Phrap软件，中心的计算能力和服务质量已有一定的保证。中心对于一些比较落后的计算设备正在进行改造升级, 同时增加一些必要的服务器，以便更好地为科研提供优质服务。

    大型计算器及其它服务器的配置，各种生物信息学平台的建立为生科院深入开展生物信息学和计算生物学的研究打下了好的基础。

The Introduction of the Bioinformation Center of SIBS

        Bioinformation Center was established in June of 2000. As the major biotechnological support center of the Shanghai Institutes for Biological Sciences, the Bioinformation Center has taken on a lot of key-projects and services, including the key-projects in the State 863, 973 high biotechnology plans, as well as projects from the Chinese Academy of Sciences, collaborating with other Universities and Research centers for a lot of projects in the bioinformatics researches. The center has also developed a lot biological databases and analysis softwares. At the same time, it undertakes the international collaboration and the integrated database query system – SRS package has been installed on the server in the Center. Dozens of international famous public databases, such as EMBL, NCBI, Swiss-Prot etc., have already achieved daily update. Our web site, www.biosino.org, has become one of the most important and popular web sites about bioinformatics in China.

        Up to now, the Center has two SGI Servers, one of them is SGI Altix350 system with 1.4GHz 32CPUs, 128GB Memory and 6TB RAID, another is Origin2000, 8CPUs, 8G memory, 600G RAID; a Dell PowerEdge 1750 Server 3.2GHz 10CPUs, 10G Memory, 750G RAID; three SGI 02 workstations. Blast, phrap parallel softwares have already been installed on the SGI Server. Among them, the high performance Blast software HP-BLAST is on the top for the related operation speed in national wide. There are over 40 Single, double CPUs servers, one 4 nodes, 8CPUs SGI-PC-Cluster, one 16 nodes, 32CPUs SW-Cluster in the Center, it is mainly used for the parallel, high performance and high speed SW-Blast software that we developed by ourselves. Therefore, the calculation ability and the service quality have been improved dramatically.

        The researches at our Center are much diversified, including the information integration, database development, protein structure analysis, algorithm development and application, biochip analysis, gene annotation and functional analysis, protein function and interaction prediction analysis etc. Currently, we have developed automatic text mining tool -- Smartlit, protein function and interaction prediction system: www.ddib.org. The staffs in our Center have participated in the important research projects, such as rice genome project and SARS research project, and have been as the first authors for those papers published on Nature and Science. Currently, we are studying the protein-protein interaction network in cells of human being, yeast, and Arabidopsis et al. with our developed system, combining with other information resources. With our unique systems, we can predict most of the unknown proteins’ functions and build their interaction networks; we are also developing the systems for the gene regulation network in cells. At the same time, we are building the models of the human diseases by using our systems with the experimental data. Our Center has also participated in the PSI (Proteomics Standard Initiative) of the international proteomics projects and is the major player in bioinformatics field for the international Human Liver Proteomics Project (HLPP). We have built the proteomics data management system and other related systems, and proteomics data analysis is one of our current top research fields.

中心所提供的服务（Services）：

在线服务包括：
GCG：综合性商业序列分析软件，包括序列比对、数据库检索、进化、基因预测、作图、pattern查找、引物设计、蛋白分析、核酸二级结构预测、翻译 Insight II： 分子结构模建分析软件
SRS：生物类数据库搜索（核酸蛋白序列及相关、免疫、转录因子、目录、文献、三维结构、基因组、突变、作图、SNP、代谢途径） BLAST & PARA_BLAST：序列比较查询软件，
数据库有：GenBank分子分类库及物种分类库、PDB、Uniprot/SWISSPROT&Trembl
EMBOSS：免费综合性分析软件，功能类似GCG
ClustalW：多序列的比对
GenScan：发现基因组中的基因
GenSplice：预测基因中Splice位点
PSIPred：预测蛋白质的结构，主要是二级结构
GlimmerM：预测小型真核生物中的基因
CDNAP：序列搜索，偏向于开发应用
BioEClone：电子克隆拼接pcr全长
TMPP：跨膜蛋白结构预测
SNP Research：用于SNP序列的比较和分析
其中，CDNAP，BioEClone，TMPP， SNP Research为本中心开发的应用系统。

非在线服务包括：
蛋白质组数据分析 、芯片数据分析 、蛋白质相互作用 、生物学数据库 等。 合作的单位包括：南方基因中心、上海芯片公司、上海大学、上海师范大学、上海生物信息中心、植生所、生化细胞所、基因中心、中山医院、蛋白质组中心等。

                         合作项目的比例为：

中心承担和参与的研究项目(Ongoing projects)：

国家重大专项：
    肝脏蛋白质组学（HLPP）计划：人类肝脏蛋白质组生物信息学研究及系列数据库构建 （The Bioinformatics Studies and the Related Databases Construction in  Human Liver Proteome Project）

973项目：
    人类重大疾病的蛋白质组学研究 (The Proteomic Studies of Human Severe Diseases)
    生命科学若干前沿与交叉问题研究 (The Advanced and Interdisciplinary Studies for Some Life Science Questions)
    基因功能预测的系统发育分析模型与检验方法 (The Systematic Analysis Models and Test Methods for Gene Function Prediction)
    多基因病的系统生物学研究 (The Systems Biology Studies of Multiple-gene Diseases)

863项目：
    国家生物信息基地建设 (The Establishment of the National Bioinformatics Bases)
    蛋白质组研究技术平台的建立及其在癌症研究中的应用 (The Construction of Proteomics Platforms and Their Applications in Cancer Research)
    生物信息学理论及应用 (The Bioinformatics Theories and Their Applications)
    中国人群遗传多样性数据库的建立 (The Construction of Genetic Diversity Database for Chinese Populations)
    利用蛋白质组学的方法鉴定诱导免疫反应的异种用源蛋白 (The Identification of Hetero-proteins inducing Immuno-reaction with Proteomics Method)

中科院重要方向和知识创新项目：
    中国核酸序列数据库 (The Chinese DNA Database)
    后基因组大规模功能解析 (The Large-scale Functional Analysis in Post-genomic Era)

国家自然科学基金：
    基于数据库的信号转导的模拟及动态展示 (The Construction of the Signal Transduction and Their Modeling and Reappearance)

上海市科委：
    Rho GDI 2介导的神经干细胞分化信号转导机制研究 (The Study of Signal Transduction Mechanism during Rho GDI 2 induced Neuro-Stem Cell Differentiation)
    人类重大疾病的系统生物学研究子课题 (The Systems Biology Study of Human Severe Diseases)
    生物信息学数据整合与挖掘 (The Integration and Data Mining of the Bioinformatic Data)

中心已发表的文章(Publications)：

1. Molecular Evolution of the SARS Coronavirus During the Course of the SARS Epidemic in China  Science Vol.303 : 1666-1669, 2004

2. The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data  Nature Biotechnol. Vol.22(2): 177-179,2004

3. A high-throughput approach for subcellular proteome: identification of rat liver proteins using subcellular fractionation coupled with two-dimensional liquid chromatography tandem mass spectrometry and bioinformatic analysis. Mol Cell Proteomics.  Vol.3(5):441-55, 2004

4. Detection of genome-wide DNA polymorphisms in Rice.  Plant Physiology Vol. 135(3): 1206 -1220, 2004

5. Identification of Alternatively Spliced mRNA Variants Related to Cancers by Genome-wide ESTs Alignment. Oncogene advance online publication 29 March 2004.

6. Association between alcohol, smoking and HLA-DQA1*0201 genotype in psoriasis.  Acta Biochim Biophys Sin (Shanghai). Vol.36(9): 597-602, 2004

7. Semantic Search among Heterogeneous Biological Databases Based on Gene Ontology, Acta Biochim et Biophysica Sinica, Vol.36(5):365-370, 2004

8. Nucleocapsid protein of SARS coronavirus tightly binds to human cyclophilin A, Biochemical and Biophysical Research Communications, in print.

9. A Novel Domain-based Method to Predict the Functional Class of Proteins (Accepted by Sci China) 

10. Scoring hidden Markov models to discriminate beta-barrel membrane proteins. Comput Biol Chem. Vol.28(3):189-94, 2004

11. mRNA expression profiling reveals a role of Helicobacter pylori vacuolating toxin in escaping host defense.  World J Gastroenterol  Vol.10(10):1528-1532, 2004

12. Analysis of gene expression profile in gastric cancer cells stimulated with Helicobacter pylori isogenic strains. J Med Microbiol.  Vol.53(Pt 10):965-974, 2004

13. A 3D model of SARS_CoV 3CL proteinase and its inhibitors design by virtual screening.  Acta Pharmacologica Sinica   Vol.24(6):497-504, 2003

14. Identification of the probable genomic packaging signal sequence from SARS-CoV genome by bioinformatics analysis.  Acta Pharmacologica Sinica Vol.24 (6). 489-496, 2003

15. Small envelope protein E of SARS: cloning, expression, purification, CD determination and bioinformatics analysis.  Acta Pharmacologica Sinica Vol.24(6). 505-511, 2003

16. Identification of an epitope of SARS-Coronavirus nucleocapsid protein  Cell Research Vol. 13(3). 141-145，2003

17. Putative hAPN receptor binding sites in the SARS_CoV spike protein.  Acta Pharmacologica Sinica Vol.24(6). 481-488, 2003

18. Prediction of beta-turns with learning machines. Peptides. Vol.24.(5):665-9, 2003

19. Support vector machine for predicting alpha-turn types. Peptides. Vol.24(4):629-30, 2003

20. A HMM-based method to predict the transmembrane regions of beta-barrel membrane proteins. Comput Biol Chem.  Vol.27(1):69-76, 2003

21. Prediction of prokaryotic promoters based on prediction of transcriptional units. Acta Biochim Biophys Sin (Shanghai).  Vol.35(4):317-24, 2003

22. TSSOM: Transmembrane Segments Prediction By Self-Organizing Map*.  Chinese Journal of Electronics. 2003

23. A scalable data mining architecture for bioinformatics, In: Data Mining IV, UK：Wessex Institute of Technology Press, 2003.12

24. A preliminary phylogenetic analysis of 14 coding sequences from SARS virus and other coronaviruses. J Genet Mol Bio.  Vol.14: 90-94, 2003

25. Performance analysis of methods that predict transmembrane regions  Acta Biochim Biophys Sin (Shanghai).  Vol.34(3):285-90, 2002

26. Construction of a proteomic map database  Acta Biochim Biophys Sin (Shanghai)..   Vol.34(2):209-14, 2002

27. Prediction Protein Structural Classes by a neural network Method”. Internet Electronic Journal of Molecular Design. Vol.1(7): 332-338, 2002

28. Performance Analysis of Methods that Predict Transmembrane        Regions”, ACTA BIOCHMICA et BIOPHYSICA SINICA, 34(3):285-290, 2002

29. 跨膜蛋白拓扑结构预测的研究进展. 国外医学生物医学工程分册, 197-201, 2001

30. 基于动态规划的跨膜蛋白疏水图比对研究.高技术通信. Vol.11:1-4, 2001

31. Research on several prediction methods of membrane protein structure and topology, High Technology Letters, Vol.3:1-4, 2001

32. An improved algorithm for transmembrane protein prediction：The Sixth International conference for Yonger Computer Scientists, 485-488, 2001

33. Using neural networks for prediction of domain structural classes. Biochimica et Biophsica Acta. Vol.14: 1-2, 2000

34. Using Neural Network for Lane-Tracking of DNA Sequencing  Slab Gels. Journal of Biochemical and Biophysical Method, Vol.45:65-74, 2000