ABSTRACT
Next-generation sequencing has allowed identification of millions of somatic mutations in human cancer cells. A key challenge in interpreting cancer genomes is to distinguish drivers of cancer development among available genetic mutations. To address this issue, we present the first web-based application, consensus cancer driver gene caller (C), to identify the consensus driver genes using six different complementary strategies, i.e., frequency-based, machine learning-based, functional bias-based, clustering-based, statistics model-based, and network-based strategies. This application allows users to specify customized operations when calling driver genes, and provides solid statistical evaluations and interpretable visualizations on the integration results. C is implemented in Python and is freely available for public use at http://drivergene.rwebox.com/c3.
ABSTRACT
The exact positioning of the membrane in transmembrane (TM) proteins plays important functional roles. Yet, the structures of TM proteins in protein data bank (pdb) have no information about the explicit position of the membrane. Using a simple hydrophobic lipid-protein mismatch energy function and a flexible lipid/water boundary, the position of lipid bilayer for representative TM proteins in pdb have been annotated. A web server called MAPS (Membrane Annotation of Protein Structures; available at: http://www.boseinst.ernet.in/gautam/maps) has been set up that allows the user to interactively analyze membrane-protein orientations of any uploaded pdb structure with user-defined membrane flexibility parameters.
Subject(s)
Algorithms , Cell Membrane/chemistry , Cell Membrane/metabolism , Computational Biology/education , Computational Biology/methods , Humans , Hydrophobic and Hydrophilic Interactions , Internet , Lipid Bilayers/chemistry , Lipid Bilayers/metabolism , Membrane Proteins/chemistry , Membrane Proteins/metabolism , Molecular Sequence Annotation , User-Computer InterfaceABSTRACT
The Korean Bioinformation Center (KOBIC) is a national bioinformatics research center in Korea. We developed many bioinformatics algorithms and applications to facilitate the biological interpretation of OMICS data. Here we present an introduction to major bioinformatics resources of databases and tools developed at KOBIC. These resources are classified into three main fields: genome, proteome, and literature. In the genomic resources, we constructed several pipelines for next generation sequencing (NGS) data processing and developed analysis algorithms and web-based database servers including miRGator, ESTpass, and CleanEST. We also built integrated databases and servers for microarray expression data such as MDCDP. As for the proteome data, VnD database, WDAC, Localizome, and CHARMM_HM web servers are available for various purposes. We constructed IntoPub server and Patome database in the literature field. We continue constructing and maintaining the bioinformatics infrastructure and developing algorithms.
Subject(s)
Computational Biology , Genome , Korea , ProteomeABSTRACT
Genotyping Tool for Viral SEQuences (GTVseq) provides scientists with the genotype information on the viral genome sequences including HIV-1, HIV-2, HBV, HCV, HTLV-1, HTLV-2, poliovirus, enterovirus, flavivirus, Hantavirus, and rotavirus. GTVseq produces alternative and additive genotype information for the query viral sequences based on two different, but related, scoring methods. The genotype information produced is reported in a graphical manner for the reference genotype matches and each graphical output is linked to the detailed sequence alignments between the query and the matched reference sequences. GTVseq also reports the potential 'repeats' and/or 'recombination' sequence region in a separated window. GTVseq does not replace completely other well-known genotyping tools such as NCBI's virus sequence genotyping tool (http://www.ncbi. nlm.nih.gov/projects/genotyping/formpage.cgi), but provides additional information useful in the confirmation or for further investigation of the genotype(s) for the newly isolated viral sequences.
Subject(s)
Enterovirus , Flavivirus , Genome, Viral , Genotype , Orthohantavirus , HIV-1 , HIV-2 , Human T-lymphotropic virus 1 , Human T-lymphotropic virus 2 , Poliovirus , Recombination, Genetic , Research Design , Rotavirus , Sequence Alignment , VirusesABSTRACT
Genotyping Tool for Viral SEQuences (GTVseq) provides scientists with the genotype information on the viral genome sequences including HIV-1, HIV-2, HBV, HCV, HTLV-1, HTLV-2, poliovirus, enterovirus, flavivirus, Hantavirus, and rotavirus. GTVseq produces alternative and additive genotype information for the query viral sequences based on two different, but related, scoring methods. The genotype information produced is reported in a graphical manner for the reference genotype matches and each graphical output is linked to the detailed sequence alignments between the query and the matched reference sequences. GTVseq also reports the potential 'repeats' and/or 'recombination' sequence region in a separated window. GTVseq does not replace completely other well-known genotyping tools such as NCBI's virus sequence genotyping tool (http://www.ncbi. nlm.nih.gov/projects/genotyping/formpage.cgi), but provides additional information useful in the confirmation or for further investigation of the genotype(s) for the newly isolated viral sequences.
Subject(s)
Enterovirus , Flavivirus , Genome, Viral , Genotype , Orthohantavirus , HIV-1 , HIV-2 , Human T-lymphotropic virus 1 , Human T-lymphotropic virus 2 , Poliovirus , Recombination, Genetic , Research Design , Rotavirus , Sequence Alignment , VirusesABSTRACT
Distributed architectures support increased load on popular web sites by dispatching client requests transparently among multiple servers in a cluster. Packet Single-Rewriting technology and client address hashing algorithm in ONE-IP technology which can ensure application-session-keep have been analyzed, an improved request dispatching algorithm which is simple, effective and supports dynamic load balance has been proposed. In this algorithm, dispatcher evaluates which server node will process request by applying a hash function to the client IP address and comparing the result with its assigned identifier subset; it adjusts the size of the subset according to the performance and current load of each server, so as to utilize all servers' resource effectively. Simulation shows that the improved algorithm has better performance than the original one.
ABSTRACT
The Internet is becoming an important way of delivering medical and other educational information. We have estabilished neuroanatomy education website in Korean (http://anatomy.yonsei.ac.kr/neuro-web/home.htm) based on textbook of medical neuroanatomy written by the authors. For searching database indexed text and figures, Microsoft SQL (Structure Query Language) server version 7.0 on the Microsoft Windows NT platform was used. HTML (hypertext markup language) template files were designed to show the results of database queries. The bulletin board was added to answer the questions. Log file analysis of the website server revealed average 112.3 visitors per day viewing average 26.1 pages in the period of four weeks from September 1st to 28th, 2001. Much appreciation was expressed in bulletin boards as well as questions and comments. We have reported process of website development for other educators in anatomy in order to share the lessons learned to develop and enhance their own information through the Internet.
Subject(s)
Education , Internet , NeuroanatomyABSTRACT
Collecting, managing and processing course material requires of much costs and efforts while they include a variety of data types particularly in the health field. Some engineering work on the material may help reduce the workload and costs to some extent. With such benefits having in mind, this paper tries to develop multimedial database for the course material of Oral Pathology in dental schools. It provides structured analysis of data for the course material, in which a unit of disease is a central class with relation to many other classes. It also achieved data independence from server applications by using the method concept of object-oriented database(OODB), which will increase reusability of the course data. Using another important concept of OODB, the system devised many functional utilities on an Internet web server including lecture notes, case studies, disease search, and question and answer, and shows how they are operated. But the effectiveness for the part of student users may remain to be evaluated.
Subject(s)
Humans , Internet , Learning , Pathology, Oral , Schools, DentalABSTRACT
Objective To realize the application of mini-PACS based on Web.Methods According to the actuality of our hospital,the reasonable structure of Database,Network Topol and application program are designed.Conclusion The cheap cost and reasonable design is the key of mini-PACS' application to hospitals.