Bioinfo Services

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-The bioinformatic facility aims to provide the research groups located within CEINGE, with a large selection of software tools, useful in the analysis of nucleic acid and protein sequence as well as other typical biological data, such as images. +The bioinformatic facility aims to provide a large selection of software tools, useful in the analysis of nucleic acid and protein sequences as well as other typical biological data, such as images.
 +The described services are currently offered to researchers located in variuos institutions in the area of Napoli, including DBBM, IGB, BIOGEM, DBPCM. Most services are also made available to the research community through our public web site http://bioinfo.ceinge.unina.it, although with some limitations due to data not publicly available and to the excessive load that a public server would pose for programs requiring higher processing power.
-The available tools include the full EMBOSS package, a vast collection of general purpose and more specific sequence handling programs, database search programs, such as FASTA and BLAST, CLUSTALW, programs from the PHYLIP package, a number of programs typically used for protein modelling and RNA structure analysis. Most programs are easily accessible through a Web interface, although command line access remains an option for researchers more familiar with the Unix interface. Fast and prompt execution of the programs is guaranteed by a 112 processor cluster, acting in concert with a number of smaller, multiprocessor servers; program execution is transparently uploaded to the cluster without any specific intervention from the user. +==What is available ?==
-A web application developed within the group, CAPRI, allows access to the programs in a global, collective application which is run on the server, but from the point of view of the user it behaves as a typical desktop application, running on each client connected to the system. +[[Bioinfo programs]]: Over 200 programs for DNA and protein sequence manipulation, molecular prediction, and statistical data analysis are currently installed and maintained. They may be grouped as follows:
 +:*[[EMBOSS]]
 +:*[[PHYLIP]]
 +:*[[HMMER]]
 +:*[[BLAST]]
 +:*[[SRS]]
 +:*[[ENSEMBL]]
 +:*[[CAPRI]]
 +:*[[PROGsDB]]
 +[[SRS databases|Databases]]: About 70 public databases are mirrored locally and daily updated. [[SRS]] is used as the main web interface for accessing these biological databases. The complete list of all the available databases on SRS is available [http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+databanks here]. Databases may be grouped according to the content into:
 +:*[[DNA databases]]
 +:*[[Gene-related databases]]
 +:*[[Protein databases]]
 +:*[[Protein-related databases]]
 +:*[[Ontology databases]]
 +:*[[Metabolic pathway databases]]
 +:*[[Reference databases]]
 +[[CEINGE facilities|Local facilities]]: Several DBs have been developed in order to support the activity of internal facilities, and their interaction with the users. The DBs offer a web interface and are generally connected to other bioinformatic analysis tools.
 +:*[[SEQSERVICE]]
 +:*[[OLIGOS]]
 +:*[[CELLBANK]]
 +[[Research DB]]:The following DBS have been developed within specific research projects, and ar currently in use by the people involved. Some of them (*) have been made available to the scientfic community as a public access web site.
 +:*[[DG-CST]]*
 +:*[[KINWEB]]*
 +:*[[EYEDIS]]
 +:*[[CFTR]]
 +:*[[CARDIODISEASE]]
-About 100 public databases are stored in-house, and the data are kept updated by mirroring: every night updates are downloaded from their primary repositories and integrated with the already available data. Access to the databases is through the SRS interface, also installed and maintained locally by the bioinformatic group (http://srs.ceinge.unina.it); the SRS installation available at CEINGE is one of the most complete in the world in terms of number of databases available and linked tools. The whole ENSEMBL genome browser, complete with all fully sequenced genomes, is also mirrored locally and made available to the users (http://ensembl.ceinge.unina.it). +{{footer|footername=footer_main}}
- +
-The described services, are currently offered to researchers located in other institutions in the area of Napoli, including DBBM, IGB, BIOGEM, DBPCM. Most services are also made available to the research community through our public web site http://bioinfo.ceinge.unina.it, although with some limitations due to data not publicly available and to the excessive load that a public server would pose for programs requiring higher processing power.+
- +
-*About 100 public databases are maintained and updated daily.+
-*Over 200 programs available for DNA and protein sequence manipulation, molecular prediction, and statistical data analysis.+
-*The laboratory is involved in the SCOPE and LITBIO national projects, aimed to use the national GRID for biological data analysis.+
- +
-==The available tools==+
- +
-*[[EMBOSS]]+
-*[[PHYLIP]]+
-*[[BLAST]]+
-*[[SRS]]+
-*[[SRS databases|Databases]]+
-*[[ENSEMBL]]+
-*[[CAPRI]]+
-*[[PROGsDB]]+
-*[[CEINGE facilities]]+
-*[[Research DB]]+
-*[[SEQSERVICE]]+
-*[[OLIGOS]]+
-*[[CELLBANK]]+
-*[[DG-CST]]+
-*[[KINWEB]]+
- +
-==DBs for specialized research projects==+
-*[[ONCOEMAT]]+
-*[[EYEDIS]]+

Current revision

The bioinformatic facility aims to provide a large selection of software tools, useful in the analysis of nucleic acid and protein sequences as well as other typical biological data, such as images. The described services are currently offered to researchers located in variuos institutions in the area of Napoli, including DBBM, IGB, BIOGEM, DBPCM. Most services are also made available to the research community through our public web site http://bioinfo.ceinge.unina.it, although with some limitations due to data not publicly available and to the excessive load that a public server would pose for programs requiring higher processing power.

[edit] What is available ?

Bioinfo programs: Over 200 programs for DNA and protein sequence manipulation, molecular prediction, and statistical data analysis are currently installed and maintained. They may be grouped as follows:

Databases: About 70 public databases are mirrored locally and daily updated. SRS is used as the main web interface for accessing these biological databases. The complete list of all the available databases on SRS is available here. Databases may be grouped according to the content into:

Local facilities: Several DBs have been developed in order to support the activity of internal facilities, and their interaction with the users. The DBs offer a web interface and are generally connected to other bioinformatic analysis tools.

Research DB:The following DBS have been developed within specific research projects, and ar currently in use by the people involved. Some of them (*) have been made available to the scientfic community as a public access web site.


Bioinformatics: Bioinformatic services - Research Activity - IT Services - The Bioinformatics Group
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