Web-based tools

NLP systems are being developed to address the increasingly challenging problem of data mining for systems level content from the published literature, that is, integrating across the global expert database of biomedical research [71]. One recent approach to this problem was to develop a web-based tool, PubNet, that is able to visualize concept and theme networks derived from the PubMed literature [72]. 

PRIO is a web-based tool intended to be used to preventively reduce risks to human health and the environment from chemicals. The aim of PRIO is to facilitate in the assessment of health and environmental risks of chemicals so that people who work as environmental managers, purchasers and product developers can identify the need for risk reduction. To achieve this PRIO provides a guide for decision-making that can be used in setting risk reduction priorities. 

A very useful tool is the Emrys Knowledge Database, representing a collection of detailed protocols for reactions performed with Biotage (Personal Chemistry) instmments. To date, this web-based tool contains around 4000 entries. 

Key Words Chemoinformatics databases information systems web-based tools computational tools combinatorial chemistry. 

Software and Web-based tools for analyzing, annotating, managing, and mining information from alarge number of biological and chemical sources. 

Virtual Fragment Scanning Current Trends, Applications and Web-based Tools... 

These results were used to screen a virtual database of primary amine fragments to enhance binding affinity in the P3 pocket using a related scaffold as shown in Figure 9.15. The virtual screening was quickly accomplished through Merck s in-house web-based tools described in Section 9.6 and was in fact a test of these tools. 

To help ensure acceptance, existing instmments should be used or modified appropriately wherever possible. Web-based tools are particularly suitable. If new instmments are required, then pilots and training programs should be planned in good time. In principle, preference should be given to quick, pragmatic, individual solutions. 

MetATT University of Alberta A web-based tool for time-series and two-factor metabolo-mic data analysis (http //metatt.metabolomics.ca/MetATT/)... 

Chen WH, Sun PP, Lu Y et al (2011) MimoPro a more efficient Web-based tool for epitope prediction using phage display libraries. BMC... 

Hohman M et al (2009) Novel web-based tools combining chemistry informatics, biology and social networks for drug discovery. Drug Disc Today 14 261-270... 

Louise-May S, Bunin B, Ekins S (2009) Towards integrated web-based tools in drug discovery. Touch Brief Drug Discov 6 17-21... 

In recent years, several Web-based tools were created in order to circumvent experimental work for epitope mapping using TCLs and TCCs. As T cell epitopes and some B cell epitopes in food allergens represent short linear peptides, prediction of these epitopes was made feasible. A summary of immunoinformatic resources including in silico T cell prediction was recently published (Korber et al., 2006). 

Web-based tool for -demonstrating query rewriting and view generation GUI-based tools used to capture user 5" actions while modifying schemas ... 

Searching for Similar Conserved Motifs Using the DoOPSearch Web-Based Tool... 

Schultz, J., R. R. Copley, T. Doerks, C. R Ponting, and P. Bork. 2000. SMART A web-based tool for the study of genetically mobile domains. Nucleic Acids Res 28 231-4. 

SNPper is a Web-based tool developed by the Children s Hospital Informatics Program, Boston [31]. The SNPper tool maps dbSNP refSNPs to known genes, allowing SNP searching by name (e g., using the dbSNP rs name) or by the golden path... 

Riva, A. A., and I. S. Kohane. 2001. A web-based tool to retrieve human genome polymorphisms from public databases. Proc AMIA Symp 558-62. 

There are many Web sites and downloadable programs that are freely available to the public (table 9.2). An early Web-based tool, RNAit, was an application created for the selection of RNAi targets in Trypanosoma brucei [22]. Chalk, Wahlestedt, and Sonhammer [14] developed a software tool that incorporates a set of Stockholm rules for siRNA design. The tool is called siSearch and allows the user to select from the following hst of design rules for selecting siRNAs ... 

Redmond, S., J. Vadivelu, and M. C. Field. 2003. RNAit An automated Web-based tool for the selection of RNAi targets in Trypanosoma brucei. Mol Biochem Parasitol 128 115-8. 

Henschel, A., F. Buchholz, and B. Habermann. 2004. DEQOR A web-based tool for the design and quality control of siRNAs. Nucleic Acids Res 32 W113-20. 

Structure-Activity Analysis is an exploratory tool which performs single linkage clustering analysis for small molecules and their biological screening information in a "heatmap" style display. With this web based tool, a list of assays may be... 

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