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Applied Bioinformatics

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This hands-on, jump-start course on analysis and quantification of biological and clinical data is addressed to busy researchers, physicians, graduate, medical, undergraduate students, and other health care or biomedical professionals. Special courses for high school students, teachers  and general public will be provided along with basic biological concepts. This is nether a software development, nor a statistics course. This is how to install and use top-notch, cutting edge open source bioinformatics software tools, in a production environment. The topics are:

BioINFO 102 - Image Analysis and Quantification

BioINFO 103 - Gene Expression Microarray Analysis

BioINFO 104 - In-Silico Protein and Gene Processing with EMBOSS

BioINFO 105 - 3D Analysis of Biomolecular Crystal Structures

BioINFO 103 - Gene Expression Microarray Analysis

We are made out of approximately 6 X10^13 cells, and each cell has two sets of ~ 3.2 billion nucleotides that makes our DNA. Approximately 5% of in DNA contains genes, which expressed and transcribed as RNA,  determines the identity and function of each cell, and of the entire organism. RNA expression profiling is paramount for discovering functional correlation between genes in normal and diseased state. The 20000 genes expressed generate an overwhelming amount of data that needs to be placed in a biological context, and sorted out in a meaningful, reproducible manner. In this section we will explore practical aspects of microarray analysis, using as pivot TM4 Microrarray Software Suite. Since very elaborate and expensive experiments have placed their raw data-sets in public databases such as OMNIBUS database or  Array Express, using Open Source tools we are going to reanalyze data from few top notch, best designed experiments. We will try as first step to reproduce the authors analysis and results, then we will formulate new hypothesis and re-explore the same data. In order to identify patterns in gene expression you are going to apply clustering algorithms (e.g. hierarchical clustering, k-means clustering) or neural-network-based divisive clustering such as self organizing maps (SOM), principal component analysis and other modern techniques. This course is hands-on, directed to newcomers that needs functional usage of the software. This is not a statistic course, having good handle of the application will allow you to explore multiple facets of analysis, explore your own data with ease and confidence, and allow more productive interaction with bioinformatics professionals and statisticians. We want to help you gain confidence and break the barrier into bioinformatics.

Price $0.00

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BioINFO 104 - In-Silico Protein and Gene Processing with EMBOSS

Some of the most routine needs in a molecular biology laboratory are nucleotide or protein sequence alignments, finding sequence patterns, motif identification. With the advent of personal whole genome sequencing the avenues towards personalized medicine will heavily depend on bioinformatic tools. This course is built around the European Molecular Biology Open Software Suite (EMBOSS), which has hundreds of modules of top quality and usefulness.

This is a two week module - Monday, Tuesday and Thursday from 5:30 to 7:30

Price $0.00

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BioINFO 105 - 3D Analysis of Biomolecular Crystal Structures

Arguably, more important than our walk on the Moon, is the full public access to 70000 of biological macromolecular structures (proteins, nucleic acids and complex macromolecules) generated through X-ray crystalography, and reconstructed at atomic and molecular (Angstrom) resolution. The 3D structures of these biomolecules will stand at the base of new and more complete integration and understanding of human physiology and pathology, and the promise to near the entry into the era of rational drug design. These uber-gold mines are available for exploration to newcomers from general population, high school students, as well as, to top notch research biomedical scientists, physicians, and graduate students pursuing  translational or fundamental questions.

This 6 hours hands-on course will enable you to visualize and explore features of X-ray crystal generated structures using a series of Open Source applications such as PyMol and Coot. The attendants will generate 3-D images and movies of the structures, identify functional aspects of the structures, measure distances and other features of those macromolecules and if time permits, explore few attempts for rational drug design and how knowledge of 3D structure is useful.

This course is made under the assumptions that attendants are familiar with organismal, cellular and molecular organization, and good handle of basic building blocks of life: nucleotides, amionacids, lipids, carbohydrates and water. For general population, high school students and teachers we have special dedicated sessions whereby basic biological concepts will be introduced along with bioinformatics.

The courses are taught using Open Source applications running on Debian GNU/Linux Operating system. However, though most of the applications run also on Windows, MacOS or Unix, for ease and continuity, and in case you want to use your own computer for all hands-on lectures, we highly recommend you to have Debian GNU/Linux installed in your personal computer. We can install it for you at a nominal fee, teach you how to install Debian GNU/Linux (Linux 101), as a stand alone OS or as a dual boot option, along with your existing Operating System (e.g. Windows7).

Price $49.00

(price ex. vat 49)

BioINFO 102 - Image Analysis and Quantification

The quantification and analysis 2D and 3D images generated in clinical practice and biomedical research are of central importance for clinical outcome and discovery. This is a hands-on, 8 hour beginner course, aimed for physicians, nurses and researchers who will learn to quantify images generated in either clinical setting such as X-Ray, MRI, CT Scans and histopathology, or from biomedical experiments where the attendants will quantify western blots, micrographs generated from laser confocal or electron microscopy. Among few Open Source imaging tools, ImageJ is the pivot application in this course.  ImageJ is a simple yet powerful software with a myriad of plug-ins, making it a  versatile "Swiss-knife" for image quantification. ImageJ is in public domain and runs equally well on GNU/Linux, Unix, MacOS and Windows operating systems.

Price $0.00

(price ex. vat 0)