Web server

When the button "submit smiles is pressed, the SMILES string is sent to the web server of Molsoft, converted to 3D, and the 3D structure is displayed in a java molecule viewer on an automatically created web page (see Figure 2-139). Unfortunately, the Molsoft server does not support downloading of the 3D structures in a standard file format. 

The molecular editor consists of a java applet that is embedded in the HTML document. It encodes the drawing into a connection table in inol-format, which is sent to the web server. 

Such systems can reside on the organization s intranet or over the Internet. Various types of hardware and software are needed to host a website. The hardware includes switches, gateways, and routers. Software includes, among others, application servers, database servers, web servers, authentication servers, and firewalls. On the other hand, the only hardware and software... 

Horton, P., Park, K. J., Obayashi, T. et al. 2007. WoLF PSORT Protein localization predictor, Nucleic Acids Res., 35(Web Server issue) W585-W587. 

Zuker, M., Mfold web server for nucleic acid folding and hybridization prediction, Nucleic Acids Res. 2003, 31, 3406 3415... 

For example, an application that reads stock figures from a newsfeed can be wired up to a spreadsheet this component does some calculations and passes the results to a database, from which a Web server extracts information on demand. Each of these components may be a stand-alone application, perhaps even with its own user interface, but is provided with a way to interact with other software. 

In our view, architecture is not only about Gothic-scale structures but is also about all structures and relationships used down to the level of code.1 The decision to use a four-tier structure, with a thin client, a Web server, a business application server, and a database, is architectural. But, in the extreme, we consider a consistent use of getXQ and setX(x) methods also to be part of the (detailed) architecture. This view leads to a somewhat less formal definition of architecture. 

Clients Browsers and traditional GUIs can connect using HTTP to a Web server. 

Web server This tier forwards appropriate requests to a servelet, a request handler that uses a standard API to plug in to the Web server. It translates CGI-encoded requests into proper method calls using distributed object invocations on an enterprise component. Then it formats and returns the results to the client. 

UNIGENE web server (1999) http //www.ncbi.nlm.nih.gov/UniGene/index.html. 

Qaude, J. B., Suhre, K., Notredame, C., Qaverie, J. M., and Abergel, C. (2004) CaspR a web server for automated molecular replacement using homology modelling. Nucleic Acids Res. 32, W606-609. 

Suhre, K. and Sanejouand, Y. H. (2004b) ElNemo a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res. 32, W610-614. 

Shulman-Peleg A, Shatsky M, Nussinov R et al (2008) MultiBind and MAPPIS web-servers for multiple alignment of protein 3D-binding sites and their interactions. Nucleic Acids Res 36 W260... 

Madsen A0 (2006) SHADE web server for estimation of hydrogen anisotropic displacement parameters. J Appl Crystallogr 39 757-758... 

Wu, C.I., and Kasif, S. (2005) GEMS a web server for biclustering analysis of expression data. Nucleic Acids Res. 33, W596-W599. 

Chemscape Server is a communication device that allows a Web server to communicate with ISIS/Host for performing registration, searching, and browsing across a variety of chemical, textual, and relational database types. 

Selected World Wide Web Servers Related to Protein Structures and Sequences3... 

S Hoersch, C. Leroy, N. Brown, M Andrade, and C. Sander, Trends Biocbent Sci. 25, 33-35 (2000) The Gene Quiz Web Server. ... 

Several useful sites for doing RNA structure analysis are available on the web. Most of the tasks described below can be performed with the Vienna RNA web server [3] at http / / rna. tbi. uni vie. ac. at /. Currently, it offers web access to the RNAfold, RNAalif old, and RNAinverse programs whose command line usage is shown below. 

Web servers are also a good starting point for novice users since they generally provide a more intuitive interface. Moreover, the Vienna RNA server returns the... 

Web servers are not ideal for analyzing many or very long sequences. Command line tools, on the other hand, are ideally suited for automating repetitive tasks. They can even be combined in pipes to process the results of one program with another. 

Another area of concern for the FDA relates to records sent over public networks, dial-up connections, or public phone lines, accessed through extemal/intemal web servers or by database servers. A number of security issues need to be considered in order to keep these records trustworthy. Intranets may face similar security issues if remote users connect to the central network resources through a local link to an Internet, even when password-protected access for the users is provided to just a small portion of a private network. These systems are considered by the agency as Open Systems (Part 11.30)4. For example, the Internet provides a convenient medium to connect to other networks, but it does not provide reliable security features, such as entity authentication, or protection from hostile users or software. 

One of the authors (Becknel) looked at host characterization based on port mixes. We developed the following visualizations to help in the process. The log scale on flows helps when there are large differences in flow volumes among ports. The data was NOT filtered by protocol and there is noise in the port fields for some protocols, especially ICMP and possibly others. Figures 9-11 show apparently normal behaviors for a workstation, a mail server, and a web server. 

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