Table of Contents |
| Preface | vii |
1. | Innovations for Personalized Medicine | 1 |
1.1. | Requirements for Personalized Medicine / Hasso Plattner, Matthieu-P. Schapranow, Franziska Häger | 1 |
1.1.1. | Researchers / Hasso Plattner, Matthieu-P. Schapranow, Franziska Häger | 3 |
1.1.2. | Clinicians / Hasso Plattner, Matthieu-P. Schapranow, Franziska Häger | 5 |
1.1.3. | Patients / Hasso Plattner, Matthieu-P. Schapranow, Franziska Häger | 6 |
1.2. | Interdisciplinary Teams / Hasso Plattner, Matthieu-P. Schapranow, Franziska Häger | 6 |
1.3. | Trends in Hardware / Hasso Plattner, Matthieu-P. Schapranow, Franziska Häger | 9 |
1.4. | In-memory Technology Building Blocks / Hasso Plattner, Matthieu-P. Schapranow, Franziska Häger | 13 |
1.4.1. | Combined Column and Row Store / Hasso Plattner, Matthieu-P. Schapranow, Franziska Häger | 14 |
1.4.2. | Complete History / Hasso Plattner, Matthieu-P. Schapranow, Franziska Häger | 14 |
1.4.3. | Lightweight Compression / Hasso Plattner, Matthieu-P. Schapranow, Franziska Häger | 14 |
1.4.4. | Partitioning / Hasso Plattner, Matthieu-P. Schapranow, Franziska Häger | 15 |
1.4.5. | Multi-core and Parallelization / Hasso Plattner, Matthieu-P. Schapranow, Franziska Häger | 16 |
1.4.6. | Active and Passive Data Store / Hasso Plattner, Matthieu-P. Schapranow, Franziska Häger | 16 |
1.4.7. | Reduction of Layers / Hasso Plattner, Matthieu-P. Schapranow, Franziska Häger | 17 |
1.5. | High-performance In-memory Genome Platform / Hasso Plattner, Matthieu-P. Schapranow, Franziska Häger | 17 |
1.5.1. | Application Layer with Micro Applications / Hasso Plattner, Matthieu-P. Schapranow, Franziska Häger | 19 |
1.5.2. | Platform Layer / Hasso Plattner, Matthieu-P. Schapranow, Franziska Häger | 21 |
1.5.3. | Data Layer / Hasso Plattner, Matthieu-P. Schapranow, Franziska Häger | 22 |
1.6. | Structure of the Work / Hasso Plattner, Matthieu-P. Schapranow, Franziska Häger | 22 |
1.7. | References / Hasso Plattner, Matthieu-P. Schapranow, Franziska Häger | 25 |
| Part I Data Processing in Personalized Medicine / Hasso Plattner, Matthieu-P. Schapranow, Franziska Häger | |
2. | Modeling Genome Data Processing Pipelines / Hasso Plattner, Matthieu-P. Schapranow, Franziska Häger | 31 |
2.1. | Introduction / Marie Schäffer | 31 |
2.2. | Related Work / Marie Schäffer | 32 |
2.3. | Modeling of Genome Data Processing Pipelines / Marie Schäffer | 35 |
2.3.1. | Requirements Engineering / Marie Schäffer | 36 |
2.3.2. | Modeling of Execution Semantics / Marie Schäffer | 38 |
2.3.3. | Machine Readable Model Representation / Marie Schäffer | 43 |
2.4. | Application Example / Marie Schäffer | 46 |
2.4.1. | Pipeline Configuration User Interface / Marie Schäffer | 46 |
2.4.2. | Data Format for Pipelines / Marie Schäffer | 48 |
2.5. | Evaluation and Discussion / Marie Schäffer | 50 |
2.6. | Conclusion and Outlook / Marie Schäffer | 52 |
2.7. | References / Marie Schäffer | 53 |
3. | Scheduling and Execution of Genome Data Processing Pipelines / Marie Schäffer | 55 |
3.1. | Introduction / Cornelius Bock | 55 |
3.2. | Related Work / Cornelius Bock | 56 |
3.3. | Method / Cornelius Bock | 59 |
3.3.1. | Requirements of the Execution Environment / Cornelius Bock | 59 |
3.3.2. | In-memory Database as Scheduler / Cornelius Bock | 60 |
3.3.3. | Real-time Scheduling / Cornelius Bock | 62 |
3.4. | Application Example / Cornelius Bock | 65 |
3.4.1. | Architecture / Cornelius Bock | 65 |
3.4.2. | Application of Design Patterns / Cornelius Bock | 69 |
3.4.3. | Implementations of Scheduling Policies / Cornelius Bock | 70 |
3.5. | Evaluation and Discussion / Cornelius Bock | 73 |
3.6. | Conclusion and Outlook / Cornelius Bock | 73 |
3.7. | References / Cornelius Bock | 74 |
4. | Exchanging Medical Knowledge / Cornelius Bock | 75 |
4.1. | Introduction / Franz Liedke | 75 |
4.2. | Related Work / Franz Liedke | 76 |
4.2.1. | In-memory Databases / Franz Liedke | 76 |
4.2.2. | Sharing Medical Knowledge / Franz Liedke | 77 |
4.2.3. | Requirements / Franz Liedke | 79 |
4.3. | Application Example / Franz Liedke | 80 |
4.3.1. | Use Case / Franz Liedke | 80 |
4.3.2. | System Requirements / Franz Liedke | 80 |
4.3.3. | Installing Applications / Franz Liedke | 83 |
4.3.4. | Configuring Applications / Franz Liedke | 85 |
4.3.5. | Cohort Analysis / Franz Liedke | 86 |
4.4. | Benchmarks / Franz Liedke | 87 |
4.4.1. | Method / Franz Liedke | 87 |
4.4.2. | Results / Franz Liedke | 90 |
4.5. | Evaluation and Discussion / Franz Liedke | 90 |
4.5.1. | Predicate Scan / Franz Liedke | 92 |
4.5.2. | Aggregation / Franz Liedke | 93 |
4.5.3. | Join / Franz Liedke | 94 |
4.6. | Conclusion and Outlook / Franz Liedke | 96 |
4.7. | References / Franz Liedke | 99 |
5. | Billing Processes in Personalized Medicine / Franz Liedke | 101 |
5.1. | Introduction / Joseph Bethge | 101 |
5.2. | Related Work / Joseph Bethge | 103 |
5.3. | Requirements Engineering / Joseph Bethge | 104 |
5.3.1. | Entity Definition / Joseph Bethge | 104 |
5.3.2. | Free Price System / Joseph Bethge | 106 |
5.3.3. | Calculation of Usage Fees / Joseph Bethge | 107 |
5.3.4. | In-memory Database Technology / Joseph Bethge | 108 |
5.4. | Application Example / Joseph Bethge | 110 |
5.4.1. | Database Schema / Joseph Bethge | 110 |
5:4.2. | Database Functionality / Joseph Bethge | 112 |
5.4.3. | User Interface / Joseph Bethge | 113 |
5.4.4. | Billing Process / Joseph Bethge | 114 |
5.5. | Benchmarks / Joseph Bethge | 115 |
5.6. | Evaluation / Joseph Bethge | 117 |
5.6.1. | Impact of Transaction Log Size / Joseph Bethge | 118 |
5.6.2. | Impact of Data Partitioning / Joseph Bethge | 119 |
5.7. | Conclusion and Outlook / Joseph Bethge | 120 |
5.8. | Appendix / Joseph Bethge | 121 |
5.9. | References / Joseph Bethge | 122 |
| Part II Real-Time Data Analysis in Personalized Medicine / Joseph Bethge | |
6. | Real-time Analysis of Patient Cohorts / Joseph Bethge | 127 |
6.1. | Introduction / Ricarda Schüler | 127 |
6.2. | Related Work / Ricarda Schüler | 128 |
6.2.1. | Cohort Analysis / Ricarda Schüler | 128 |
6.2.2. | K-Means Clustering / Ricarda Schüler | 130 |
6.2.3. | Hierarchical Clustering / Ricarda Schüler | 131 |
6.2.4. | In-memory Technology Building Blocks / Ricarda Schüler | 132 |
6.3. | Application Example / Ricarda Schüler | 133 |
6.3.1. | Architecture / Ricarda Schüler | 133 |
6.3.2. | Application / Ricarda Schüler | 133 |
6.4. | Benchmarks / Ricarda Schüler | 137 |
6.4.1. | Benchmark Data / Ricarda Schüler | 137 |
6.4.2. | Benchmarks for In-memory Technology / Ricarda Schüler | 139 |
6.4.3. | Benchmarks for R / Ricarda Schüler | 140 |
6.4.4. | Impact of Selected Variables / Ricarda Schüler | 142 |
6.4.5. | Test Procedure and Technical Environment / Ricarda Schüler | 142 |
6.5. | Results and Discussion / Ricarda Schüler | 143 |
6.5.1. | Data Size / Ricarda Schüler | 144 |
6.5.2. | Number of Genes / Ricarda Schüler | 147 |
6.6. | Conclusion and Outlook / Ricarda Schüler | 149 |
6.7. | References / Ricarda Schüler | 151 |
7. | Ad-hoc Analysis of Genetic Pathways / Ricarda Schüler | 153 |
7.1. | Introduction / Dominik Müller | 153 |
7.2. | Related Work / Dominik Müller | 154 |
7.2.1. | Pathway Analysis / Dominik Müller | 156 |
7.2.2. | Existing Analysis Possibilities / Dominik Müller | 157 |
7.2.3. | Storing a Graph / Dominik Müller | 158 |
7.2.4. | NoSQL / Dominik Müller | 159 |
7.2.5. | In-memory Database Technology / Dominik Müller | 160 |
7.3. | Creating an Integrated Pathway Database / Dominik Müller | 161 |
7.4. | Application Example / Dominik Müller | 165 |
7.5. | Benchmarks / Dominik Müller | 167 |
7.5.1. | Occurrences of Analyzed Genes / Dominik Müller | 169 |
7.5.2. | Genes in Input Set / Dominik Müller | 169 |
7.5.3. | Integrated Pathways / Dominik Müller | 170 |
7.6. | Results and Discussion / Dominik Müller | 170 |
7.6.1. | Occurrences of Analyzed Genes / Dominik Müller | 170 |
7.6.2. | Genes in Input Set / Dominik Müller | 171 |
7.6.3. | Integrated Pathways / Dominik Müller | 172 |
7.7. | Conclusion and Outlook / Dominik Müller | 174 |
7.8. | Appendix / Dominik Müller | 175 |
7.9. | References / Dominik Müller | 178 |
8. | Combined Search in Structured and Unstructured Medical Data / Dominik Müller | 181 |
8.1. | Introduction / David Heller | 181 |
8.2. | Related Work / David Heller | 182 |
8.3. | In-memory Database Text Analysis Features / David Heller | 185 |
8.4. | Application Example / David Heller | 186 |
8.4.1. | Customized Biomedical Dictionaries / David Heller | 187 |
8.4.2. | Customized Extraction Rules / David Heller | 188 |
8.4.3. | Post-processing of Text Analysis Results / David Heller | 190 |
8.4.4. | Trial Filtering / David Heller | 191 |
8.4.5. | User Interface / David Heller | 192 |
8.5. | Benchmarks / David Heller | 193 |
8.5.1. | Genes / David Heller | 195 |
8.5.2. | Partitioning the Text Analysis Result Table / David Heller | 196 |
8.5.3. | Indexed Trials / David Heller | 196 |
8.6. | Discussion / David Heller | 197 |
8.7. | Conclusion and Outlook / David Heller | 201 |
8.8. | Appendix / David Heller | 202 |
8.9. | References / David Heller | 204 |
9. | Real-time Collaboration in the Course of Personalized Medicine / David Heller | 207 |
9.1. | Real-time Combination of Oncology Data / Hasso Plattner, Matthieu-P. Schapranow | 207 |
9.1.1. | Holistic Patient View / Hasso Plattner, Matthieu-P. Schapranow | 209 |
9.1.2. | Search in Structured and Unstructured Data / Hasso Plattner, Matthieu-P. Schapranow | 210 |
9.1.3. | Real-time Analysis of Patient Cohorts / Hasso Plattner, Matthieu-P. Schapranow | 211 |
9.2. | Building Research Hypotheses / Hasso Plattner, Matthieu-P. Schapranow | 211 |
9.3. | Pharmaceutical Feedback Loop / Hasso Plattner, Matthieu-P. Schapranow | 212 |
9.4. | Federal Bureau of Statistics / Hasso Plattner, Matthieu-P. Schapranow | 213 |
9.5. | Health Insurance Companies / Hasso Plattner, Matthieu-P. Schapranow | 214 |
9.6. | Tumor Board of the Future / Hasso Plattner, Matthieu-P. Schapranow | 214 |
9.7. | References / Hasso Plattner, Matthieu-P. Schapranow | 216 |
| List of Abbreviations / Hasso Plattner, Matthieu-P. Schapranow | 217 |
| Index / Hasso Plattner, Matthieu-P. Schapranow | 221 |