Query Server

Transaction servers systems, also known as query server systems, provide an interface to which clients can send requests to perform an achon, in response to which they execute the action and send back results to the client. 

Most clinical data management systems used for clinical trials today store their data in relational database software such as Oracle or Microsoft SQL Server. A relational database is composed of a set of rectangular data matrices called tables that relate or associate with one another by certain key fields. The language most often used to work with relational databases is structured query language (SQL). The SAS/ACCESS SQL Pass-Through Facility and the SAS/ACCESS LIBNAME engine are the two methods that SAS provides for extracting data from relational databases. 

While the protocol described above has proven very useful in its own right, it often serves as the first step in designing custom protocols for a team. Once a user is satisfied with the results returned by the ad hoc query, the next step is often to hardwire these queries into a protocol that provides one-button access to all the pertinent data for a project. Figure 5 shows such a protocol used to retrieve data for several assays in a Neuroscience project. This protocol highlights an additional filtering option that we make use of in many of our protocols. The text box ( selected cmpds from list ) (7) supports the input of a list of identification numbers (in our case either jnjnumber or batchid ). This allows data to be retrieved on select compounds as opposed to all those tested in the assays. This feature is very popular and involves the use of Perl within the Pipeline Pilot protocol. All this work is done on the server and the results are written to a SD file that can be downloaded to the desktop. At this stage either DIVA or Accord for Excel is typically used to view the files. 

The Sequence Retrieval System (Etzold et ah, 1996) is a network browser for databases at EBI. The system allows users to retrieve, link, and access entries from all the interconnected resources such as nucleic acid, EST, protein sequence, protein pattern, protein structure, specialist/boutique, and/or bibliographic databases. The SRS is also a database browser of DDBJ, ExPASy, and a number of servers as the query system. The SRS can be accessed from EBI Tools server at http // www2.ebi.ac.uk/Tools/index.html or directly at http //srs6.ebi.ac.uk/. The SRS permits users to formulate queries across a range of different database types via a single interface in three different methods (Figure 3.4) ... 

Figure 8.2. Query page for searching metabolic pathway between two compounds. A search for metabolic pathway(s) between two compounds in a specific organism can be performed at the KEGG server.

Analysis (PSA) server of BMERC predicts secondary structures and folding classes from a query sequence. On the PSA home page at http //bmerc-www.bu.edu/psa/ index.html, select Submit a sequence analysis request to submit the query sequence and your e-mail address. The returned results include (a) probability distribution plots (conventional X/Y and contour plots) for strand, turn, and helix and (b) a list of structure probabilities for loop, helix, turn, and strand for every amino acid residues. 

The prediction of the secondary structures can be made by the structure similarity search of PDB collection at the site. Several servers provide such prediction method. The Jpred, which aligns the query sequence against PDB library, can be accessed at http //jura.ebi.ac.uk 8888/index.html. To predict the secondary structures, however, check Bypass the current Brookhaven Protein Database box and then click Run Secondary Structure Prediction on the home page of Jped to open the query page (Figure 12.10). Upload the sequence file via browser or paste the query sequence into the sequence box. Enter your e-mail address (optional) and click the Run Secondary Structure Prediction button. The results with the consensus structures are returned either online (linked file) or via e-mail (if e-mail address is entered). 

The 3D-PSSM (Kelley et ah, 2000) server at http //www.bmm.icnet.uk/ 3dpssm/ offers online protein fold recognition. On the submission form, enter your e-mail address and a one-line description of the query protein, then paste the query sequence into the sequence box and click the Submit button. The query sequence is used to search the Fold library for homologues. You will be informed of the URL where the result is located for 4 days. The output includes a summary table (hits with statistics models that can be viewed with RasMol classifications and links) and fold recognition by 3D-PSSM with a printout as exemplified in Figure 12.13. The alignment displays consensus sequence, secondary structures (C for coil, E for extended, and H for helix), and core score (0 for exterior to 9 for interior core). 

The CBS prediction server also provides services for predicting O-glycosylation sites (NetGly) in mammalian proteins (http //www.cbs.dtu.dk/services/NetQGly-2.0/) and phosphorylation sites (NetPhos) in eukaryotic proteins (http //www.cbs.dtu.dk/ services/NetPhos/). Paste the query sequence and click the Submit Sequence button to receive the predicted results. NetOGly returns tables of potential versus threshold assignments for threonine and serine residues as well as a plot of O-glycosylation potential versus sequence position. NetPhos returns tables of context (nanopeptides, [S,T,Y] + 4 residues) and scores for serine/threonine/tyrosine predictions. 

The ProtSite search can be conducted at ScanProsite tool (selecting Scan a sequence for the occurrence of PROSITE patterns) of ExPASy Proteomic tools (http //www.expasy.ch/tools/scnpsite.html), or PPSearch of EBI (http //www2.ebi.ac. uk/ppsearch/) or ProfileScan server (http //www.isrec.isb-sib.ch/software/PFSCAN form.html). On the search form, paste the query sequence, select options (e.g., display in PPSearch and databases in ProfileScan) and click the Run/Start the Scan button. The search results are returned (after clicking SEView applet button in ProfileScan) with different outputs as shown in Figure 12.16. 

The PANAL/MetaFam server (http //mgd.ahc.umn.edu/panal/run panal.html) analyzes protein sequence for Prosite patterns, Prosite profiles, BLOCKS, PRINTS, and Pfam. Check the options, paste the query sequence, and click the Submit button. The analytical results are returned with a graphical sketch of the predicted features,... 

Eukaryotic sequences were suitably aligned, then one of them was used as a query to search for finished and unfinished prokaryotic genomes via a BLAST server. If several homologs were found in a single species, only the most similar one was chosen for alignment. In the basis of the BLAST hit, the annotated complete sequence was retrieved from the finished genome when available. 

The web clients are often called thin clients in the enterprise application, because they do not directly query databases, execute complex business logic, or connect to legacy applications. Such heavyweight operations are off-loaded to the components in the web tier or business tier underneath in order to utilize the security, speed, service, and reliability provided by J2EE server-side technologies. The thin-client design makes the enterprise application scalable, and the development process simple and flexible. 

The rapidly growing number of three-dimensional coenzyme biosynthesis enzyme stmctures in the public domain and the cognate publications are best addressed via the internet server of Brookhaven Protein Data Bank (http /Avww.rcsb.org/pdb/home/ home.do). Queries can be targeted to individual enzymes or to entire pathways. 

Windows Internet Name Service (WINS) WINS provides a database for the storage and retrieval of NetBIOS computer names. Each client must register with the WINS server to be able to be added to and query the database. 

The presentation server provides the query capabilities and the visualization of data to the end-users and to other applications. 

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