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RRX Pharma-Bioinformatics Future Challenges in Bioinformatics.

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Presentation on theme: "RRX Pharma-Bioinformatics Future Challenges in Bioinformatics."— Presentation transcript:

1 RRX Pharma-Bioinformatics Future Challenges in Bioinformatics

2 RRX Pharma-Bioinformatics Introduction Introduction: How RRX got involved … Life sciences context: How bioinformatics came to be important… The past half century: How bioinformatics has evolved…

3 RRX Pharma-Bioinformatics Introduction Categories of Bioinformatics Tools Why We Need Supercomputers Software Development Issues Future Challenges Tools for Biotech Projects Summary

4 RRX Pharma-Bioinformatics How RRX got involved … Submitted a Canadian Foundation for Innovation (CFI) proposal for Advanced Bioinformatics Collaborative Computing (ABioCC)

5 RRX Pharma-Bioinformatics How RRX got involved … Developed an SVG based visualization front end Paper will be presented at SVG Open 2003 in Vancouver on July 17th

6 RRX Pharma-Bioinformatics How bioinformatics came to be important… After the structure of DNA was reverse engineered with X-Ray diffraction in 1953 focus shifted to nucleic acid sequence analysis DNA/RNA/protein sequence data accumulated using computer programs for storage and analysis

7 RRX Pharma-Bioinformatics How bioinformatics came to be important… Bioinformatics algorithms in development for the last half century came into wide spread use by researchers The ability to compare sequences created a homology context for unknown sequences of interest leading to advances…

8 RRX Pharma-Bioinformatics How bioinformatics came to be important… Improved sequencing technology enabled the complete deciphering of the human genome >>> 1999 About 3.18 billion base pairs Celera used 300 PE Biosystems ABI Prism 3700 DNA Analysers

9 RRX Pharma-Bioinformatics How bioinformatics has evolved… Central dogma of molecular biology – –DNA sequences are transcribed into mRNA sequences, mRNA sequences are translated into protein sequences, which fold 3D creating structures with functions statistically survival selected >>> affecting the prevalence of the underlying DNA sequences in a population

10 RRX Pharma-Bioinformatics How bioinformatics has evolved… This created a supporting information flow –Organization and control of genes in the DNA sequence –Identification of transcriptional units in the DNA sequence –Prediction of protein structure from sequence –Analysis of molecular function

11 RRX Pharma-Bioinformatics How bioinformatics has evolved… Another covariant information flow was created based on the scientific method –Create hypothesis wrt biological activity –Design experiments to test the hypothesis –Evaluate resulting data for compatibility with the hypothesis –Extend/modify hypothesis in response

12 RRX Pharma-Bioinformatics How bioinformatics has evolved… IT used to handle explosion of data from high throughput techniques, too complex for manual analysis –X-ray diffraction

13 RRX Pharma-Bioinformatics How bioinformatics has evolved… –Automated DNA sequencing Amersham Biosciences Applied Biosystems Beckman Coulter LI-COR SpectruMedix Corp. Visible Genetics Corp.

14 RRX Pharma-Bioinformatics How bioinformatics has evolved… –Microarray expression analysis

15 RRX Pharma-Bioinformatics How bioinformatics has evolved… Rapid emergence of 3D macromolecular structure databases –New sub discipline: structural bioinformatics Atomic and sub cellular spatial scales –Representation/physics –Storage/retrieval/source data correlation/interpretation –Analysis/simulation –Display/visualization

16 RRX Pharma-Bioinformatics How bioinformatics has evolved…

17 RRX Pharma-Bioinformatics Categories of Bioinformatics Tools… Databases >>> search/compare Sequence Analysis - Clusters Genomics Phylogenics Structure Prediction Molecular Modelling Microarrays Packages, Misc Apps, Graphics, Scripts

18 RRX Pharma-Bioinformatics aceperl BLAST Blastall Blastpgp BLAT Blimps Entrez FASTA fastacmd formatdb getz HMMER IMPALA InterProScan PHI-BLAST ProSearch PSI-BLAST PSI-BLASTN Seguin Swat tace xace Categories of Bioinformatics Tools… Database >>> search/compare

19 RRX Pharma-Bioinformatics Sequence Analysis Artemis Bl2seq BLAST Clustal W, X consed/autofinish Cross_match Dotter EMBOSS FASTA Glimmer HMMER InterProScan MEME View Paracel Transcript Assem Phrap Phred Primers ProSearch Readseq2 Rnabob RRTree SAPS seals Seqsblast STADEN Swat T-Coffee

20 RRX Pharma-Bioinformatics Genomics Calc_primers Cross_match FPC GENSCAN Glimmer Image Mzef Phrap Phred STADEN Swat tace tace_celegans tRNAscan-SE xace xace_celegans

21 RRX Pharma-Bioinformatics Phylogenics Clustal W Clustal X MOLPHY MrBayes PHYLIP RRTree T-Coffee TREE-PUZZLE TreeViewX

22 RRX Pharma-Bioinformatics Structure Prediction EMBOSS MEME Modeller Mzef PHI-BLAST

23 RRX Pharma-Bioinformatics Molecular Modelling Modeller –homology modeling an alignment of a sequence to be modeled with known related structures Rasmol –a molecular graphics program intended for 3D visualisation of proteins and nucleic acids Raster3D (publishing images) X3DNA –analyzing and rebuilding 3D structures

24 RRX Pharma-Bioinformatics Microarrays Dapple –a program for quantitating spots on a two- colour DNA microarray image.. OligoArray –a program that computes gene specific oligonucleotides that are free of secondary structure for genome-scale oligonucleotide microarray construction.

25 RRX Pharma-Bioinformatics Packages, Useful Scripts/Source Code, Graphics, PERL BioPERL BioJava boxshade mvscf seg Split_fasta povRay Raster3D MOLPHY

26 RRX Pharma-Bioinformatics Why We Need Supercomputers… Some commercial packages run on supercomputers –Accelrys: modeling and simulation Materials Studio Cerius 2 (SGI Unix only) –Homology modeling to catalyst design Insight II (SGI Unix only) –3D graphical environment for physics based molecular modeling Catalyst (high end Unix servers) –database management valuable in drug discovery research QUANTA (high end Unix servers) –crystallographic 2D/3D protein structure solution Discovery Studio

27 RRX Pharma-Bioinformatics Why We Need Supercomputers… Supercomputer advantages –Multiple processors –Large shared memory –Handle very large files –Large/fast RAID arrays –Terabyte tape backup systems –Power backup systems –High performance networks

28 RRX Pharma-Bioinformatics Why We Need Supercomputers… Common bioinformatics requirements –Computationally intensive tasks –Large memory models –Intensive/complex database searches –Large experimental database sets –Large derived database sets –Large persistent intermediate data structures –Teamwork data sharing and visualization

29 RRX Pharma-Bioinformatics Why We Need Supercomputers… Network requirements –Driving gigE/10gigE NICs Moving large files/data sets rapidly Visualization streams/Access GRID Coordinating Cluster/GRID computing Dynamic provisioning of light paths

30 RRX Pharma-Bioinformatics Why We Need Supercomputers…

31 RRX Pharma-Bioinformatics Why We Need Supercomputers… xxxxxxxxxxxxxxxxxxxxxxx

32 RRX Pharma-Bioinformatics Software Development Issues… Collaboration contexts/barriers –Team work … collaboration spaces –Standards development … DTDs –Integration issues… experimental data to homology to 3D model platform issues… network issues – 9k MTU - jumbo frames –Licensing issues – public vs. private

33 RRX Pharma-Bioinformatics Future Challenges… Creating developer infrastructure for building up structural models from component parts … –components from macromolecule libraries ported to object models Understanding the design principles of systems of macromolecules and harnessing them to create new functions … –specialized molecular machines

34 RRX Pharma-Bioinformatics Future Challenges… Learning to design drugs efficiently and cost effectively based on knowledge of the target … –target generation automation –validation automation Development of enhanced simulation models that give insight into context based function from knowledge of structure … –possible use of artificial intelligence to limit scope of search

35 RRX Pharma-Bioinformatics How Tools might be used for Industry Biotech Projects

36 RRX Pharma-Bioinformatics Summary Bioinformatics –well positioned to assist with application development –exploring novel bioinformatics software development –proceeding with supporting access GRID and optical switching technology

37 RRX Pharma-Bioinformatics Questions/Comments… ? ;-)


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