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Future Challenges in Bioinformatics

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Presentation on theme: "Future Challenges in Bioinformatics"— Presentation transcript:

1 Future Challenges in Bioinformatics
RRX Pharma-Bioinformatics

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

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

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

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

6 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 RRX Pharma-Bioinformatics

7 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… RRX Pharma-Bioinformatics

8 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 RRX Pharma-Bioinformatics

9 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 RRX Pharma-Bioinformatics

10 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 RRX Pharma-Bioinformatics

11 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 RRX Pharma-Bioinformatics

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

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

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

15 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 RRX Pharma-Bioinformatics

16 How bioinformatics has “evolved”…
RRX Pharma-Bioinformatics

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

18 Categories of Bioinformatics Tools…
Database >>> search/compare 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 RRX Pharma-Bioinformatics

19 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 RRX Pharma-Bioinformatics

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

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

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

23 Molecular Modelling Modeller Rasmol Raster3D (publishing images) X3DNA
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 RRX Pharma-Bioinformatics

24 Microarrays Dapple OligoArray
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. RRX Pharma-Bioinformatics

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

26 Why We Need Supercomputers…
Some commercial packages run on “supercomputers” Accelrys: modeling and simulation Materials Studio Cerius2 (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 RRX Pharma-Bioinformatics

27 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 RRX Pharma-Bioinformatics

28 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 RRX Pharma-Bioinformatics

29 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 RRX Pharma-Bioinformatics

30 Why We Need Supercomputers…
RRX Pharma-Bioinformatics

31 Why We Need Supercomputers…
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32 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 RRX Pharma-Bioinformatics

33 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 RRX Pharma-Bioinformatics

34 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 RRX Pharma-Bioinformatics

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

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

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

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