Course

The course provides an introduction to pharmaceutical bioinformatics, which includes chemobioinformatics in relation to drugs, omics, chemical biology, protein function, databases, sequence analysis, proteins and their interactions, chemical descriptions of proteins, peptides and organic compounds, statistical experimental design, data modeling, QSAR, proteochemometrics, and drug discovery and development.

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Screen shot from the course overview on the course on Pharmaceutical Bioinformatics, showing different lectures.

The course is taken entirely on the Internet via a web-browser. Each course section consists of lectures in form of slides, written texts, and audio presentations. The written materials and audio is accompanied with slides, making them similar to follow as a normal oral lecture. The written materials is also down-loadable as printable pdf:s for those who rather like to read texts off-line.

The lecture section are intermingled with online tutorials, questionares, Bioclipse exercises and assignments. For examples of Bioclipse exercises taught in the course, click here.

Throughout the course a teacher will be available for questions via email, and the teacher will correct your assignments and give comments.

There are no fixed schedules, which means that you can take the course entirely at your own pace.

The course is complemented with the course book Introduction to Pharmaceutical Bioinformatics which contains and overview of the field pf Pharmaceutical Bioinformatics with coverage of all facets of this highly interdisciplinary field. (For information on the book click here.)

At the end of the course there is an examination in form of a written task that the student will complete and submit for examination to receive a pass, pass with distinction or no pass. Each student will receive a different task.

Course content

  • Lecture 1: Introduction to Pharmaceutical Bioinformatics
  • Lecture 2: Pharmaceutical Bioinformatics – a Course Overview
  • Lecture 3: Representing Molecules in Computers
  • Lecture 4: Databases in Pharmaceutical Bioinformatics
  • Lecture 5: Statistical Experimental Design
  • Lecture 6: Structure Descriptors, Physical and Chemical Data
  • Lecture 7: Macromolecular Descriptors
  • Lecture 8: Alignments in Bioinformatics
  • Lecture 9: Representation of 3D Structure
  • Lecture 10: Methods of Data Analysis
  • Lecture 11: Bioinformatics with Bioclipse
  • Lecture 12: Rule Based Learning and Rough Sets
  • Lecture 13: QSAR and Proteochemometrics
  • Lecture 14: Validation of Models
  • Lecture 15: Lead identification and Optimization

The course is divided into the 15 topics shown above; each covering a distinct area important for understanding the discipline pharmaceutical bioinformatics. Each week, there will be audiovisual or standard presentations with detailed lecture notes and suggested readings related to the weekly subject(s). There will be compulsory and optional assignments in the form of quizzes, multiple choice and short answer questions. The assignments are checked by teacher(s) who give individual feedback to each student. Communication between participants and teacher(s) takes place mainly via email.

Workload

The course can be started every Monday and lasts for ten weeks at half-time study load (10 weeks /50% workload), but can be adjusted for 5 weeks / 100% study load if you wish to rush the studies, or 20 weeks / 25% study load, if you wish to combine the studies with a regular work or other studies. (I.e. in the latter cases the lectures are started twice a week, or every other week, rather than one every week).

Examination

After successful completion of the assignments in the course, a final written examination will be issued to give feed-back on the student’s understanding of the course.

Certificate

Course participants that pass the final examination will be awarded certificates from Uppsala University for successful completion of the commissioned course on Pharmaceutical Bioinformatics.