Analysis Tools for

Hu Z, Mellor J, Wu J, DeLisi C. VisANT an online visualization and analysis tool for biological interaction data. JiMC Bioinformatics 2004 5 17. 

We have been developing cutting-edge data analysis tools for the pharmaceutical industry for over a decade, with a particular focus in the fields of cheminformatics and bioinformatics. We now describe how our insights apply to these areas. 

TEM is a direct analysis tool for knowing if metal clusters are present in catalytic solutions. This technique permits to define the size, structure, morphology and state of aggregation of the metal particles [11]. Hence, this technique can be in particular useful to identify nanoclusters in metal-catalysed reactions, using molecular complexes as catalytic precursors. But the catalytic activity of these observed nanoclusters must be further checked. 

Nygaard [752] has evaluated the application of the Spectraspan DC plasma emission spectrometer as an analysis tool for the determination of trace heavy metals in seawater. Sodium, calcium, and magnesium in seawater are shown to increase both the background and elemental line emission intensities. Optimum analytical emission lines and detection limits for seven elements are reported in Table 5.8. 

Mass spectrometry offers a special advantage over other detection schemes for instrumental chromatography because the mass spectra of the mixture components are acquired, providing a very powerful qualitative analysis tool for these components. 

Lattimer, B.Y., Wright, M., and Cutonilli, J. 2000. Composite Fire Hazard Analysis Tool for Topside Structures (CTHAT) - Version 3." NSWCCD-TR-65-2000/32. U.S. Navy Surface Warfare Center Carderock Division, Washington, DC. 

Seo J, Gordish-Dressman H, Hoffinan EP (2006) An interactive power analysis tool for microarray hypothesis testing and generation. Bioinformatics 22 808-814. doi btk052 (pii) 10.1093/bioinformatics/btk052... 

Functionalized polymers are of interest in a variety of applications including but not limited to fire retardants, selective sorption resins, chromatography media, controlled release devices and phase transfer catalysts. This research has been conducted in an effort to functionalize a polymer with a variety of different reactive sites for use in membrane applications. These membranes are to be used for the specific separation and removal of metal ions of interest. A porous support was used to obtain membranes of a specified thickness with the desired mechanical stability. The monomer employed in this study was vinylbenzyl chloride, and it was lightly crosslinked with divinylbenzene in a photopolymerization. Specific ligands incorporated into the membrane film include dimethyl phosphonate esters, isopropyl phosphonate esters, phosphonic acid, and triethyl ammonium chloride groups. Most of the functionalization reactions were conducted with the solid membrane and liquid reactants, however, the vinylbenzyl chloride monomer was transformed to vinylbenzyl triethyl ammonium chloride prior to polymerization in some cases. The reaction conditions and analysis tools for uniformly derivatizing the crosslinked vinylbenzyl chloride / divinyl benzene films are presented in detail. 

Consideration of Surface Tool Concerns. RBS was chosen as the analysis tool for several reasons it works well on the Ti-Pt system, it provides non-destructive information about Pt distribution after implantation and after electrochemical analysis and... 

Analysis tools for three-dimensional visualization need to be developed for various microscopies and materials analysis instrumentation. 

PATRIC Virginia Bioinformatics Institute Provides rich data and analysis tools for all bacterial species in the selected NIAID category A-C priority pathogens list (http //www.patricbrc.org/portal/portal/patric/ Home)... 

VisANT Boston University Integrative visual analysis tool for biological networks and pathways (http //visant.bu.edu/)... 

Strigol has also been reported recently in root cultures of the broad-leaved herbaceous weed Menispermum dauricum54 In this way, the use of LC/MS/MS techniques has revealed a powerful analysis tool for minor compounds. By using this methodology, a new isomer of strigol, the structure yet unknown, has been detected in sorghum root exudates, and the presence of alectrol or orobanchol in cotton root exudates has been discarded.2 These results are summarized on Table 6.2. 

It is thus obvious that a systematic approach is needed, to apply PCM on a large scale. Some key factors to success can be identified, namely the use of experimental design to reduce the number of experiments and the development of proper database- and PCM-analysis tools for storage and management of data. Thus, having many thousands of potential macromolecular targets and an essentially unlimited number of interaction partners (i.e., drug-like structures, peptides, proteins, DNA,... 

Markel, T., Brooker, A., Hendricks, T., Johnson, V., Kelly, K., Kramer, B., O Keefe, M., Sprik, S., Wipke, K. (2002). ADVISOR a systems analysis tool for advanced vehicle modeling. /. Power Sources 110, 255-266. A commercial version of the software is under preparation by AVL. Graz, Austria http //wtvw.avl.com... 

Kapucu FE, Tanskanen JM, Mikkonen JE, Yla-Outinen L, Narkilahti S, Hyttinen JA (2012) Burst analysis tool for developing neuronal networks exhibiting highly varying action potential dynamics. Front Comput Neurosci 6 38... 

Oxford Molecular Group Oxford, U.K. recently introduced DIVA (a visualization and analysis tool for chemical and biological data) at the 210th ACS national meeting in San Francisco. 

Peptides for the New Millennium, [Proceedings of the 16th American Peptide Symposium, 1999], ed. G. B. Fields, J. P. Tam and G. Barany, Kluwer Academic Publishers, Dordrecht, Netherlands, 2000 P. A. Keifer, NMR Analysis Tools for the Peptide Sciences , p. 396... 

Mass spectrometry is sensitive, rugged, and has the ability to provide extensive qualitative and quantitative information. Mass spectrometry also provides a large dynamic range, can be automated, and has a fast analysis time. These characteristics have made mass spectrometry a very powerful and attractive analysis tool for medicinal chemistry and combinatorial chemistry. However, not all synthetic organic compounds are readily detected by mass spectrometry, and the sensitivity can vary with the mode of ionization. As a result, sensitivity is dependent on the physical characteristics of the compound. 

S. Draghici, Data Analysis Tools for DNA Microarrays, Chapman HaU/CRC Press,... 

STM and AFM methods can be used as a nanoscale quantitative analysis tool for materials on surfaces (e.g., pollution control). This was mentioned earlier where 60 x 10 cholesterol molecules were estimated in the image. The lower limit in detection by AFM or STM is theoretically one atom or molecule (i.e., 10 mol ). This means that quantitative analysis has an extreme lower limit for detection, which is important in pollution control, etc. where very small amounts must be monitored. On this subject of the nanoanalytical application of both STM and AFM much remains to be smdied. It is obvious that in the future of nanochemistry will develop based on such nanosystem studies. The nanocrystal smdies of amino acids as described above are also another area that will develop based on these procedures. 

As well as these general motif databases, there are some more specialized sequence analysis tools for identifying particular structural or functional features. One well-studied example is that of coiled coils. The program COILS " allows one to compare a sequence against profiles derived from known parallel two-stranded coiled coils, to assess the likelihood that the query sequence is indeed a coiled coil. More involved analyses based on pairwise interactions have been developed, such as PAIRCOIL. Several families of coiled coils are actually well recognized by their PROSITE motifs. However, the leucine zipper PROSITE motif, L-X(6)-L-X(6)-L-X(6)-L, is poorly discriminating, and for this specific family of coiled coils, the program TRESPASSER provides a more refined identification... 

Life-Cycle Cost Analysis Tool for Building Protection... 

NIST. 2006b. Life-Cycle Cost Analysis Tool for Chem/Bio Protection of Buildings. Accessed on March 15, 2007, at http //www2.bfrl.nist.gov/software/LCCchembio/index.htm. 

---