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Integrative Informatics Sylabus
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GBS755 Integrative Informatics

Purpose - to train tool makers

The purpose of this course is to equip participants with understanding of informatics infrastructure for biomedical applications with practical knowledge on how to program this environment. Specifically, the participants are exposed to practical use of semantic web and cloud computing technologies and resources. A successful participation signifies that the participant is fully equipped to develop informatics applications that make the most of biomedical data resources and bioinformatics analytical services.

Rationale and history

Data integration and information modelling represent an increasingly important component of biomedical research. This tendency is accentuated by the movement towards personalization of medicine which requires that an heterogeneous ensemble of data sources and statistical computing workflows need to be invoked  to understand specific biomolecular data. Furthermore, and rather plainly, it is the informational nature of living organisms that ultimately mandates systems biology approaches to study component process. Accordingly, the training offered in this course is geared to the integrative challenge of developing computational aggregations of data sources and analytical workflows. The first versions of this course were narrowly focused on statistical computing programming environments, because the data sets used to be much smaller and more homogeneous than they are today. Its current version follows the developments in bioinformatics infrastructrue to be instead focused, just as narrowly, on browser based applications (Web2.0) served by cloud computing hosted services.  

Organization

This hands on workshop is organized to include informatics graduate students, faculty and computational staff. A limited number of slots is made available for Pathology and other graduate students pursuing non-informatics research topics with the specific intent of a) bringing informatics to those other fields and b) bringing biomedical challenges to the attention of computational centric researchers. The purpose of this arrangement is that graduate students be paired with informaticians such that a bidirectional cross-training takes place. The three hours / week contact time consist of a weekly workshop style session where each participant brings a laptop and willingness to learn and teach. The “assembler language of the web” is javascript so knowledge or willingness to learn it is an absolute requirement. The computational environment used in the course reflects that of the web in general, consisting of an assertive server side (“data”) and a functional client side (“analysis”). In addition to cloud computing, the attendants are also introduced to Semantic Web concepts. The weekly session takes place year-round and relies on information exchange environments such as a wiki, shared desktop and distributed code version control. For further detail and records of past sessions at UAB see http://uab.mathbio.org/workshop.

Evaluation

Evaluation is based on class participation and code development, tracked via distributed version control.