Algorithm and Software Development in Pharma Research

Week 1: Systems biology: a gentle introduction. Definition of systems. Comparison of natural and artificial systems. Applicability of systems theory and engineering in biology. Basic principles of regulation: positive and negative feedback. Mechanism elucidation: experimental and theoretical methodologies.

Week 2: The theory of evolution. Fundamental concepts. Evolution of macromolecular sequences, molecular phylogeny. The "Tree of Life": Perception or reality?

Week 3: Regulation of gene expression. Basic principles of genetic regulation. Nuclear receptors and their pharmacological importance. Epigenetics: was Lamarck right after all? High-throughput methodologies for transcriptome analysis (microarrays, next-generation sequencing).

Week 4: Complex kinetics. Qualitative description of dynamic processes: equilibria, steady states, periodic processes, deterministic chaos, and their relevance to biology. Quantitative description with differential equations, kinetic simulations. Examples: glycolytic oscillations, "predator-prey models".

Week 5: Metabolic control. Metabolic networks. Enzyme regulation. The concept of "metabolic flow". Signal processing in biochemical reactions. Self-optimisation in microbial metabolism.

Week 6: Pattern formation in biological systems. The chemical basis of morphogenesis. Spatiotemporal information processing.

Week 7: Evolution of networks. Ligand-receptor coevolution. The chemoton theory. System-theoretical description of evolutionary dynamics.

Week 8: Biology meets Computer Science: DNA computing, evolutionary programming, artificial life.

Week 9: Homeostasis and Robustness. The purpose of biological regulation: self-preservation in a constantly changing environment. Adaptation via Robustness.

Weeks 10-14: „Software At Your Fingertips” project: role-playing exercise to simulate an in-house software development project in pharma research. The primary objective here is not to come up with a usable application but rather to learn how to manage a scientific software development project in a tightly controlled environment.

The project will go through the following stages:-

- „Preparation”: introduction to the project, discussion of roles.

- „Kickoff meeting”: the ’programming team’ will be formed.

- „User requests”: how to manage expectations, how to formulate use cases.

- „Development meetings”: architectural planning, tools, testing procedures.

- „Convincing management”: how to present the project successfully to skeptical leaders.

- „Rollout and Maintenance”: how to manage a mature project.

The students will assume the following roles:-

- „Project Leader”: this person will manage the project and interfaces with the users and management;

- „Architect”: this person will design the application;

- „Developer”: this person will write code;

- „Tester/Maintainer”: this person will test the code and will interact with the users after product rollout;

- „User”: provides use cases, feature requirements, will complain about bugs;

- „Manager”: requests progress reports, must be convinced that the project is worthwhile, otherwise s/he fires the whole team!

Depending on the number of students, more than one project team could be formed. The lecturer will act as moderator and neutral observer.