1. Bachelor Project:
Real-time Analysis of Genome Data
July 12, 2012
Matthieu-P. Schapranow
Hasso Plattner Institute
Chair of Prof. Hasso Plattner

2. Numbers you should know
The Human Genome Project
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■ 1984: Human Genome (HG) project idea
discussed at Alta Summit as “DNA
available on the Internet”
■ 1990: HG project for 15 years started in
the US (3 billion USD funding)
■ 2000: Rough draft of the HG announced
■ 2003: Complete genome sequenced
■ 2006: Last and longest chr1 sequenced
■ As of today, we know:
□ HG consists of 3.2 Bbp (~3.2 GB),
□ 23 chromosomes,
□ 20k-25k distinct genes
Real-time Analysis of Genome Data, M. Schapranow, July 12, 2012

3. 3
Costs in USD
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Comparison of Costs
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Costs per Megabyte RAM
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Numbers you should know
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Real-time Analysis of Genome Data, M. Schapranow, July 12, 2012
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Costs per Megabase Sequencing
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Comparison of Costs for Main Memory and Genome Analysis
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4. Numbers you should know
Hardware Characteristics
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■ 1,000 core cluster,
25 TB main memory
■ Consists of 25 identical nodes:
□ 80 cores
□ 1 TB main memory
□ Intel® Xeon® E7- 4870
□ 2.40GHz
□ 30 MB Cache
Real-time Analysis of Genome Data, M. Schapranow, July 12, 2012

5. Aims of the Bachelor’s Project
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■ Gather interdisciplinary knowledge to work in
teams with biological and medical experts
■ Explore data from gene, protein, drug, and
pathway databases to gain new insights
■ Implement algorithms optimized for in-memory
technology, e.g. cluster algorithms for quantifying
similarity of samples or detection of single
nucleotide polymorphisms
■ Proof applicability of in-memory technology for
real-time analysis of genome data
■ Areas of interest: life sciences, crop sciences,
biology, crime investigation, etc.
Real-time Analysis of Genome Data, M. Schapranow, July 12, 2012

6. Your profile
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■ What we expect
□ Flexibility in working interdisciplinary
□ At least one passed database lecture
□ Knowledge in using either or all: Python, C++, Bash, SQL
■ We provide you with
□ Introduction to in-memory technology and genomics basics
□ Technology introduction in either or all: SQL, SQLScript, L, R,
BFL
Real-time Analysis of Genome Data, M. Schapranow, July 12, 2012

7. Do not hesitate to contact us!
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Matthieu-P. Schapranow, M.Sc.
schapranow@hpi.uni-potsdam.de
http://j.mp/schapranow
Hasso Plattner Institute
Enterprise Platform & Integration Concepts
Matthieu-P. Schapranow
August-Bebel-Str. 88
14482 Potsdam, Germany
Real-time Analysis of Genome Data, M. Schapranow, July 12, 2012