A.N. Belozersky Institute

  MSU Bioinformatics Portal   GeneBee

Russian EMBnet Node

The GeneBee Group

The History Of The GeneBee Group

The Group Foundation

The GeneBee Group was established in 1989 by the initiative of Leonid I.Brodsky. The goal of the GeneBee Group is a development of software packages for biological macromolecules structure analysis. L.I. Brodsky, A.L. Drachev, K.M. Chumakov, R.L. Tatuzov, ..Leontovich, A.E.Gorbalenya, E.V.Koonin were the founder-fathers of GeneBee Group whose original ideas are taken as principles of the software creation.
L.I. Brodsky

The First Release

The first package was released in 1989. It was called GeneBee and, in fact, it was the first significant national bio-computing package. Up to 1995 several versions of the package were installed on personal computers in many institutions working in the field of the molecular biology. The package was installed in more than 130 laboratories in Moscow and other cities of throughout the former Soviet Union.

The Mail Server

In 1993 GeneBee Group establish own mail server. Users were released from a necessity to keep huge databanks on their computers: they were gained the ability to send requests and receive answers by e-mail. Due to this feature the GeneBee Server started to gain popularity in other countries.

The Russian Projects

The GeneBee Group takes active participation in national Russian projects:
  • Genom-Info "Informational services of SSTP "Human genome" program members, in 1991-92 - the head of this program council was acad. Bayev ..
  • Ministry of science and SSTP "Resources of researches provision of physical and chemical biology and bio-technology in 1992-2005" - the head of this council was acad. Knorre D.G.

The Countries Which Have Sent Requests To The GeneBee Server

The Training And Consulting Activity

The GeneBee Group in collaboration with the section of Mathematical Methods in Biology of Belozersky Institute regularly holds two-days courses intended to teach users working and mastering the GCG package. Up to day 12 seminars for 100 listeners have been held. Arrangements are making for weekly consultations on the GeneBee, the GCG and the WhatIf packages. Discussion of the molecular and biological problems is also organized for takers. Preparation of the courses for the WhatIf package is carried out at present.

The Activity At The A.N.Belozersky Institute

In 1990 The GeneBee Group started to work in Belozersky Institute. Since then Belozersky Institute provide full supply with computers for the group needs, and lend comprehensive support including financial support. On the other hand, the GeneBee Group provides development, maintenance and extension of network information infrastructure in the institute.

The Grants

GrantStart-EndProject Name
RFBR 94-07-12711-m1994-1995Telecommunication service by genetic databases and by programs for their analisys.
RFBR 95-07-19298-m1995-1997Telecommunication service by genetic databases and by programs for their analisys through World Wide Web service.
RFBR 98-07-90208-B1998-2000Service of the Russian biologists and medics on Russian EMBNet node and development distributed object-oriented environment for storage and analysis of the molecular-biological information.
RFBR 01-07-90120-B2001-2003Improvement the services of biologists and medics on Russian EMBNet node. Development the graphical programming system, providing pipelining the users requests. Implementation the system for semantic analysis the information of molecular-biology databanks.
CRDF RUB1-1473-MO-042004-2009Joint Program on Research Advancement and Training in Bioinformatics.
FP6 VIZIER                        
2004-2010Comparative Structural Genomics of Viral Enzymes Involved in Replication.
INTAS IT 04-77-71782005-2007Global and Local Protein Matching.
CRDF RUB1-1657-MO-062006-2008Quality Control, ORF detection and Gene Anotation of Peanibacillus Dendriformix and Peanibacillus Vortex genomes.
RFBR 06-07-89143-a2006-2008Development of the bioinformatics portal for the support of the research in the area of the molecular and system biology.
RFBR 10-07-00685-a2010-2012Development of Bioinformatics portal of Belozersky Institute, MSU.

The Russian Users Of The GeneBee Package

InstituteAmt. InstituteAmt.
Moscow Moscow region
Institute of Molecular Biology, RAS16 Institute of Poliomyelitis and Virus Encephalitis, RAMS4
Institute of Bio-organic Chemistry, RAS11 Institute of Protein, RAS, Puschino9
Belozersky Institute of Physical and Chemical Biology, MSU18 Institute of Cell Biophysics, RAS, Puschino1
Department of Biology, MSU5 Institute of Mathematical Problems of Biology, RAS, Puschino1
Department of Chemistry, MSU2 Institute of Chemical Physics, RAS, Chernogolovka2
Department of Fundamental Medicine, MSU2 St.-Petersburg
Institute of Chemical Physics, RAS1 St.-Petersburg State University2
Bach Institute of Biochemistry, RAS2 Institute of Influenza, RAMS2
Institute of Organic Chemistry, RAS1 Kirov
Center of Oncology, RAMS4 Institute of Microbiology of Ministry of Defense2
Institute of Therapy and Tumor Diagnostics, RAMS1 Institute of Hematology and Blood Transfusion at Ministry of Health Protection1
Institute of Cancer Genesis, RAMS4 Ufa
Institute of Virus Preparations, RAMS3 Scientific Center of RAS1
Institute of Molecular Genetics, RAS5 Saratov
Institute of Electrical Chemistry, RAS2 Institute of Biochemistry and Physiology of Plants an Microorganisms, RAS1
Institute of Immunology at Ministry of Health Protection3 Kazan
Russian Medico-Genetical Scientific Center, RAMS4 Kazan State University1
Institute of Human Genetics, RAS2 Novosibirsk,
Institute of Brain, RAMS1 "Vector" at VNII of Molecular Biology of Ministry of Health an Medical Industries3
Institute of General Genetics, RAS2 Institute of Biochemistry, RAMS3
Institute of Biomedical Chemistry, RAMS4 Institute of Bio-organic Chemistry of Siberian Council, RAS2
Institute of Gene Biology, RAS3 Institute of Cytology and Genetics RAS SO4
Institute of Virology, RAMS5 VNII of Molecular Biology of Ministry of Health an Medical Industries1
Institute of Microbiology, RAS1 Ukraine, Kiev
VNII "Genetics", RAMS1 Institute of Bio-organic an Oil Chemistry, UAS2
Russian University of Friendship of Peoples1 Institute of Oncology Problems of Ukrainian Academy of Medical Sciences1
Russian State Medical University, RAMS1 Institute of Molecular Biology, UAS1
Moscow State Academy of Thin Chemical Technology, RAS1 Institute of Veterinary Medicine of Academy of Agrarian Sciences1
VAXZ of Ministry of Defense1 Ukraine, Kharkov
Science-Industrial Center "TRANSKOMP"1 AeroSpace Group "Soyuz"1
Scientific Complex "NIK"1 Institute of Urgent Surgery at Ministry of Health Protection1
Technological Group "Immunotech" at MSU1 Belorussia, Minsk
"Bioinformservice" Group1 Institute of Bio-organic Chemistry of Belorussian Academy of Sciences1
Center of Scientific and Engineering Problems1 Georgia, Tbilisi
Institute of Agricultural Biotechnology VASXNIL3 Institute of Molecular Biology and Biological Physics of Georgian Academy of Sciences1
Riga, Latvia Kazakhstan, Alma-Ata
Biomedical Center of University1 Institute of Molecular Biology and Biochemistry KazAS1
Institute of Molecular Biology of Latvian Academy of Sciences3 Institute of General Genetics an Cytology, KazAN1

The E-Mail Service Evolution

In 1992 the GeneBee Group establish in Belozersky Institute the e-mail service, as a first step only in one computer. At the same year the process of building the local network in institute was started. It was 20 computers in the network in the 1994, and 100 in 1997. To the autumn of 1999 the local network of the institute, which contain also the computers belonging to the Polymer Chemistry School of Chemistry Department of Moscow State University and Center of Molecular Medicine, consist of up to 200 computers. This network is considered to be one of the largest networks in MSU.

The GeneBee Group Web-Server

In May 1995 the GeneBee Group build the first version of web-server, which slowly becomes popular in worldwide molecular and biology society. To the winter 2001 the average number of daily requests to the GeneBee Server is more than 120. The links to services, as to the best ones, are placed in web pages of such a famous centers of molecular biology as Stanford, Heidelberg, Caroline University in Sweden, Paster Institute and also in web pages of many universities in Europe and United States. Totally there are up to 237 links to the GeneBee Services.

The EMBnet

In 1992 the GeneBee Group establish contacts with Oxford laboratory of molecular biology. In December 1996 the European Organization of Bio-computing named EMBnet (European Molecular and Biology Network), taking into account significant achievements of the GeneBee Group in field of bio-computing, affiliates Belozersky Institute and rest on the group the functions of the National Russian Node of EMBnet.

The Software At The GeneBee Server

As the Russian Node of EMBnet the GeneBee Group take efforts intended on giving access to the best software packages and sequence analysis tools to Russian specialists. Thus in 1997 the Institute bought the GCG and WhatIf packages, which are the most popular packages on field of biological polymers structure analysis. There are up to 108 registered users of the GCG package in Russia.

The Biological Databanks Presented At The GeneBee Server

There are following tools and databanks presented at the GeneBee Server and being kept up to date:

The Tools Developed By The GeneBee Group, Based On The Original Algorithms

Free Distributed Software

  • BLAST-2.0 - Basic Local Alignment Search Tool - one of the most popular programs for quick search by homologies. Developed in NCBI. In our server the basic and full versions are presented.
  • FASTA-3.3 Sensitive homology search.
  • CLUSTAL - Building of multiple alignment - basic and full versions are presented.
  • Molscript is the program for work with 3D structures of biological polymers. The world standard for preparing high quality preprints for publications.
  • DPIDB - The databank of DNA-protein complexes 3D structures (processed subset from PDB). Development in cooperation with A.N.Belozersky Institute and institute of bio-technology .
  • PSI-BLAST from NCBI - searching in sequence databanks using profiles.
  • EMBOSS - The programs set for work with biological sequences, in development by EMBnet. It is assumed that this package will leave behind by capabilities the GCG package.
  • GROMOS - Molecular dynamics package (add-on to WhatIf package).

Future Plans Of The GeneBee Group