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BioIndonesia

Introduction 

Bioinformatics represents a new field of scientific inquiry, devoted to answering questions about life science and using computational resource to answer those questions. A key goal of bioinformatics is to create database system and software platforms capable of storing and analyzing large sets of biological data. Bioinformatics in Indonesia Integrated as integral part of Modern Biotechnology development in Indonesia.


Indonesia Research Institutions currently engage in Bioinformatics


Airlangga University - Surabaya

 

Introduction to Bioinformatics course is offered at 5th semester for undergraduate students in Faculty of Biotechnology, Atma Jaya Catholic University, Jakarta, Indonesia.
Course contents: biological databases (nucleotide and amino acid sequences); alignment techniques to determine similarity degree; database searching and phylogenetic tree building; methods in phylogenetic tree building; genomics and proteomics; application and future of bioinformatics.

 

Department of Biology School of Life Sciences and Technology (SITH) Bandung Institute of Technology (ITB) offering Bioinformatics for post graduate programme


Bogor Agricultural University - Bogor

 

M.Sc. In Computer Sciences with special interest in Bioinformatics. Offered by The Graduate Program Bogor Agricultural University (IPB)


Gadjahmada University - Yogyakarta

 

Subject Proteomics and Bioinformatics included in syllabus of Biotechnology Doctoral programme


University of Indonesia - Depok

 

University of Indonesia held Bioinformatics subjects at post graduate programme in Chemistry Department, Faculty of Mathematic and Natural Sciences.

The Biomedicine programme at post graduate course of Faculty of Medicine, University of Indonesia gives some bioinformatics-related materials within its subjects. Introductory practical bioinformatics analysis materials are part of Research Methodology subject. Topics on sequence analysis are given in the Molecular Biology subject, while other wet-oriented bioinformatics activities, such as primer design and trace analysis, are given in the Molecular Biology Laboratory subject.

 

Badan Pengkajian dan Penerapan Teknologi (BPPT)


Eijkman Institute for Molecular Biology - Jakarta


Contact person: Hidayat Trimarsanto (anto@eijkman.go.id), or Ismail Eko P (eko@eijkman.go.id)
Phone: +62-21-3917131

Bioinformatics research activities at Eijkman:

  1. Data Mining: Use data mining to solve biological problem, e.g. secondary structure or protein topology prediction; antigenic determinant prediction
  2. Molecular Simulation: Protein modeling and molecular dynamics; H5N1 Hemaglutinin protein strains from Indonesia; General 3D Modeling
  3. Population dynamics and Epidemiology: Malaria drug resistance
  4. Molecular Evolution: Malaria (pfEMP1); Hepatitis B subtyping and host interaction; population database for forensic; Ethnic evolution

Software used in bioinformatics analysis:

  1. FinchTV               : edit trace file seq from ABI DNA sequencer
  2. Bioedit                 : general editing tool for multiple sequence alignment
  3. Clustal W/X         : multiple sequence alignment
  4. Perlprimer           : designing primer
  5. Primer 3               : editing primer designed
  6. ApE                       : single sequence analysis
  7. phylip                   : phylogenetic analysis
  8. Mr Bayes             :
  9. Tree Puzzle        :
  10. PAML                   :
  11. Molphy                :
  12. Tree View            :
  13. TreeDyn              :


Indonesian Institute of Science (LIPI) - Cibinong


Southeast Asian Regional Center for Tropical Biology (SEAMEO-BIOTROP) - Bogor

 

PT Charoen Pokphand Indonesia (CPI)


Bioinformatics Research at R&D Biotechnology CPI

We are focusing on EST (expressed sequence tags) genome project of the Litopenaeus vannamei shrimp, the main goal of the EST research is to obtaining relevant markers for shrimp genetic improvement with total sequence 100k ESTs from three different tissues (cephalothorax, eyestalk, and pleopod).  tools in bioinformatics such as phred, phrap, and consed are useful to  handle such a huge sequences data.

We conduct this research cooperate with academic collabolator, Department of Biology Washington University in St. Louis (Wash U). As part of human genome project institution, Wash U has experienced to sequence the genome many of organism with highly coverage and established pipeline.



Bioinformatics plays a key important to analyze and align short EST sequences into contigs and singletones.  Aligned short sequences information from ESTs indicate which genes are expressed under normal dan altered condition, thus we can compare gene expression level e.g. between healthy shrimp and shrimp infected by disease.


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