![]() For this purpose, we developed ProdoNet, an application that visualizes the functional relations within a set of prokaryotic genes or proteins with regard to the joined gene regulatory network. Although some of these tools provide advanced network analysis features, most require local installation and do not provide simple access to prokaryotic gene regulatory data.Ĭurrently, web-accessible tools for the mapping of a list of genes and corresponding proteins to the gene regulatory and metabolic network in bacteria with an intuitive visualization are missing. #Networkview 36 softwareA major strength of STRING is the visualization of obtained results, where interactions within a set of analysed proteins are displayed as undirected edges.Īpart from the described database-integrated applications, various software tools are available for the visualization of biological networks an overview was given before ( 11 ). For protein interaction analyses, the STRING website provides a sophisticated platform to indicate functional associations between proteins ( 10 ). For example, VIS-O-BAC ( 9 ) supports the functional exploration of prokaryotic genes and proteins by indicating their genomic positions, matching them onto KEGG pathways and supplying the Gene Ontology annotations. However, there are some tools available that allow searching for functional relations within a list of genes. Usually, the web interfaces of databases are capable to manage only one item per query and are not prepared to deal with a list of genes and proteins. For example, the database CoryneRegNet presents a visualization of gene regulatory networks from corynebacteria, mycobacteria and E. Several databases provide visualization features for the presented data. Some databases exclusively present data based on experimental evidence, such as PRODORIC, while other data collections also include data predicted by different algorithms, like Tractor_DB ( 5 ), ExtraTrain ( 6 ) and SwissRegulon ( 7 ). Others cover a range of species, like RegTransBase ( 3 ) or PRODORIC ( 4 ). For prokaryotes, these include databases that focus on a single model organism, as RegulonDB for Escherichia coli ( 1 ) or DBTBS for Bacillus subtilis ( 2 ). Such application should map the list of experimentally identified genes and proteins to the known transcriptional and metabolic network and be able to identify new relationships.Ī variety of databases supply valuable information on transcription factor binding sites and gene regulation. Consequently, a computer-aided application is required to explore the common functions of these genes and proteins within the complex cellular network. ![]() The challenge for the scientist is to identify the common properties between co-regulated genes, in order to understand the underlying processes within the analysed cell. In the case of transcriptome and proteome analyses, the final result is usually a list of proteins or transcripts that show significant differences in their abundance under the compared experimental conditions. ![]() After one have done the NetworkView installation, start NetworkView.īutton to open a new file.The prevalence of high-throughput technologies for the analysis of biological systems causes a strong demand on specialized software for the interpretation of the increasingly complex experimental results. Please refer to the installation instructions that come with the tool.ġ. #Networkview 36 installTo use NetworkView, one will need to download and install the tool on ones PC ( Windows NT and Windows 9x only). #Networkview 36 freeOne may visit their web sites and get a free download. Information and documents with printed maps and reports for future use. It discovers all TCP/IP nodes in a network using DNS, SNMP and ports The NetworkView is a compact network management tool from NetworkView Software, Inc. ![]() #Networkview 36 serialAtop GW51C-MAXI Serial Server is an SNMP device that allows many popular SNMP Network management platforms such as HP Open View and Sun Net Manager to conduct on the SerialManager.ĭepending on the network management tools one are using, device (GW51C-MAXI Serial Server) information can be collected from running the management tools including IP address, DNS name, system descriptions and NIC information etc. ![]()
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