Belépés címtáras azonosítással
angol nyelvű adatlap
Algorithm and Software Development in Pharma Research
A tantárgy neve magyarul / Name of the subject in Hungarian: Algoritmus- és szoftverfejlesztés a gyógyszerkutatásban
Last updated: 2010. november 9.
Mathematics and Computer Science: linear algebra, differential equations, Boolean algebra, probability theory. Web programming experience and basic understanding of database technologies is required for the practical part.
Biology: no previous knowledge is required beyond standard high-school biology. Knowledge of basic concepts such as cell structure, genome organisation, DNA and protein structure is desirable.
Two main parts are foreseen: the scientific/theoretical part will focus on the topic “Information Processing in Living Systems”, whereas the technological and cross-cultural issues will be explored in the practical exercise “Scientific Software in Pharmaceutical Research”.
Part 1 “Information Processing in Living Systems”
Living organisms exchange not only matter and energy with their environment, they also process information. The molecular mechanisms of biological regulation will be discussed, in particular gene expression regulation, qualitative and quantitative description of complex kinetic phenomena, metabolic control, signal processing in biochemical reactions, homeostasis and robustness.
Part 2 “Scientific Software in Pharmaceutical Research”
A well-balanced scientific software portfolio should have three components: commercial software, academic open-source packages, and applications developed in-house. The latter is essential to achieve competitive advantage (“if I use exactly the same tools as my competitors, my results will be very similar to theirs”). The students will work on a fictitious in-house development project “Software at your fingertips” that should present a complex scientific calculation through an intuitive Web interface. Interactions with “non-expert users” and “upper management” will be learned through role-playing exercises
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.
Lectures and project-based computer assignments.
Friedrich, P.: Supramolecular Enzyme Organization. Quaternary Structure and Beyond. Pergamon Press, Oxford/Akadémiai Kiadó, Budapest, 1984.
Lecture notes by András Aszódi.