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Architecture of large projects in bioinformatics

General data

Course ID:	1000-717ADP
Erasmus code / ISCED:	11.954 The subject classification code consists of three to five digits, where the first three represent the classification of the discipline according to the Discipline code list applicable to the Socrates/Erasmus program, the fourth (usually 0) - possible further specification of discipline information, the fifth - the degree of subject determined based on the year of study for which the subject is intended. / (0619) Information and Communication Technologies (ICTs), not elsewhere classified The ISCED (International Standard Classification of Education) code has been designed by UNESCO.
Course title:	Architecture of large projects in bioinformatics
Name in Polish:	Architektura dużych projektów bioinformatycznych
Organizational unit:	Faculty of Mathematics, Informatics, and Mechanics
Course groups:	Obligatory courses for 2nd stage Bioinformatics
Course homepage:	https://www.mimuw.edu.pl/~lukaskoz/teaching/adp/
ECTS credit allocation (and other scores):	6.00 Basic information on ECTS credits allocation principles: the annual hourly workload of the student’s work required to achieve the expected learning outcomes for a given stage is 1500-1800h, corresponding to 60 ECTS; the student’s weekly hourly workload is 45 h; 1 ECTS point corresponds to 25-30 hours of student work needed to achieve the assumed learning outcomes; weekly student workload necessary to achieve the assumed learning outcomes allows to obtain 1.5 ECTS; work required to pass the course, which has been assigned 3 ECTS, constitutes 10% of the semester student load. view allocation of credits
Language:	English
Main fields of studies for MISMaP:	biology biotechnology computer science
Type of course:	obligatory courses
Prerequisites (description):	Programming in python Basic understanding of bioinformatic concepts
Mode:	Classroom
Short description:	Knowledge of the structure of larger bioinformatic software projects. Students create a team project, learn how to use code version control systems and how to collaborate on code writing. They discuss history of development of some leading bioinformatics software packages, libraries and databases. Possible options for choice of software licenses are discussed. They talk about the role of open source and free software in scientific programs and their role in reproducibility of research.
Full description:	Data formats in bioinformatics. Popular software libraries (BioPerl, BioPython). Most important bioinformatics databases (UniProt, PDB, RefSeq, GenBank, ENA, InterPro, etc.) Software licensing for scientific purposes. Free-software licensing. Patents. Generic model Organism database (GMOD) project - assumptions, history and usage. Genome browsers, problem description and state of the solutions. High-performance computing (HPC) Version control systems (CVS, SVN, git), and online collaboration ad distribution platforms (github, sourceforge). Software testing, automated testing frameworks. Scientific workflow systems - taverna and galaxy. MyExperiment platform. Reproducible research. Literate programming idea and sweave, markdown, software documentation. Interactive scripting platforms, Rstudio, Jupyter.
Bibliography:	Materials on the website: https://www.mimuw.edu.pl/~lukaskoz/teaching/adp/
Learning outcomes:	(in Polish) - ma wiedzę o technologiach zarządzania danymi biologicznymi (K_W01) - ma wiedzę o technologiach zarządzania oprogramowaniem bioinformatycznym (K_W02) - ma podstawową wiedzę dotyczącą uwarunkowań prawnych i etycznych związanych z działalnością naukową i dydaktyczną (K_W11) - potrafi tworzyć zaawansowane procedury analizy danych ( K_U03) - umie posługiwać się systemami do tworzenia procedur bioinformatycznych (K_U04) - potrafi w przystępny sposób opisać cel, założenia i algorytm procedury bioinformatycznej (K_U05)
Assessment methods and assessment criteria:	Homework for some laboratories. Team project and a presentation on a chosen subject

Classes in period "Summer semester 2024/25" (past)

Time span:	2025-02-17 - 2025-06-08	Selected timetable range: weekly course term Go to timetable MO TU WYK LAB W LAB TH FR
Type of class:	Lab, 30 hours more information Lecture, 30 hours more information
Coordinators:	Łukasz Kozłowski
Group instructors:	Łukasz Kozłowski
Students list:	(inaccessible to you)
Credit:	Examination

Classes in period "Summer semester 2025/26" (future)

Time span:	2026-02-16 - 2026-06-07	Selected timetable range: weekly course term Go to timetable
Type of class:	Lab, 30 hours more information Lecture, 30 hours more information
Coordinators:	Łukasz Kozłowski
Group instructors:	Łukasz Kozłowski
Students list:	(inaccessible to you)
Credit:	Course - Examination Lecture - Examination

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