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Courses in Bioinformatics
(GeneBee in collaboration with Department of the Mathematical Methods in Biology)

The Role of Bioinformatics
What is GCG?
Programm of GCG Courses for Beginners
Usage of GCG Package on GeneBee Server
Examples of GCG Output Forms
What is WhatIf?
Teachers
Planned Courses
Courses Statistics
Computer Class
Consultations

The Role of Bioinformatics

Due to colaborate work of many laboratories the total length of published nucleotide sequences is now

3 500 000 000 base pairs.

The printed copy of these data would consist of 1,000 manuscrits of   1000 pages each.

Sequences are stored in public electronic data bases. The only possibility to choose and structurize nescessary information is to use bioinformatic methods.

Problem 1. Many biologists are not familiar with many existing effective computer programms.

Problem 2. There is a lack of new ideas about what new significant results can be obtained from the huge ammount of data. This ideas can be invented by biologists who are familiar with bioinformatics.

What is GCG?

GCG is a software package that contains all standard tools designed for working with biological sequences (searching information in databases, alignment, generation of philogenetic trees, primer design, secondary RNA structure prediction and lot of other).

GCG vs. Internet programms:

• Everything in one place. Easy to use utilities

• Minimal requirments to computer and network speed

• GCG is popular among the scientists

Programm of GCG Courses for Beginners
(two days)

• Review of main nucleotide and proteins sequences databases

• Introduction to Unix. GCG utilities

• Search in biological sequences databases

• Exploration of evolution relationship of sequences

• Work with anotated protein families

Number of  registered users (from Russia) - 92

Hits of package:
1998..............................................8468
1999 (up to September).................7541

	Unrooted phylogramm of the selected alcoholdehydrogenases. (Output of  paupsearch programm)
	Secondary structure of tRNA, predicted by  mfold programm

What is WhatIf?

Whatif is a software package that contains realisation of more than 2000 actions with 3D structures of macromolecules (proteins, DNA, RNA, complexes).
Authors gave such charecteristic to this package:
"WhatIf lets molecular enginier using computer ask questions like: "What if I will change this valine for isoleucine?" and find out results of such a mutation using the program ".

Advantages among other programs (Rasmol, SwissPDBviewer): the amount of features.
Disadvantage: hard to learn.

WhatIf is not a tool that is worth for visulaization of macromolecules and other simple tasks, that can be done with other programs such as Rasmol.

• About WhatIf - the one of the main packages for visualization and modification of 3D structures of proteins and nucleotide acids

• About the technology of solving main problems using all available tools (GeneBee, GCG, Internet)

Computer class

In autumn of 1998 the computer class in campus "B" was organized. This class is equiped with 8 computers Pentium that are connected to local network.

There is a gateway to Internet. There is a way to work with GCG an WhatIf packages. Programs Rasmol, Gsview and other are installed. Computer class is used for bioinformatic courses and for scientific semenars.

Consultations

Everyone who need a consultation for GeneBee service, GCG or WhatIf package is welcomed. If someone wants to get help on using mathematical methods he is welcomed also. Consultations take place weekly on Tuesday in 321app. of our institute. The time of consultations is 11am-12-am.