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Source: Daniel Coca’s Research paper

Source: Daniel Coca’s Research paper. Java Native Interface- C++- FPGA. 10 sample files upload for spectrum processing. Peak list charts for 10 spectra each within range of 70K to 250K plotting points. SVG, Ajax JavaScript canvas – Constraints? non-scalability.

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Source: Daniel Coca’s Research paper

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  1. Source: Daniel Coca’s Research paper

  2. Java Native Interface- C++- FPGA. • 10 sample files upload for spectrum processing. • Peak list charts for 10 spectra each within range of 70K to 250K plotting points. • SVG, Ajax JavaScript canvas – Constraints? non-scalability. • Java Applets with provision to zoom and pan.

  3. Java Web Services through wsdl file for uploaded spectrum and parameter file. Use of @WebServiceRef annotation • Java Web Services through JAX-WS using @WebMethod, @WebParam. Spectra and parameters passed as strings. • FASTA sequence search by memory mapped I/O in parallel.

  4. JMol structure information sent as applet param element. • Constraints? What if the protein structure is too large or if it is a genome structure. • Just pass meta-structure information to the browser. E.g. Functional groups and when the zoom operation is performed an AJAX/SVG/JSON script can render the details at atomic level.

  5. Modelling of 4.95 x 10^9 atoms should take 32 bits. • Each 4 byte value is an index to meta information about the atom as in PDB or the mmCIF format. • How to model molecular transformation, transcription for large protein/genomic sequences? • Given a chemical reaction/transformation of a polymer like protein, not all the atoms undergo dis-orientation.

  6. So derive equivalent classes for these isomorphic reaction types and perform vector transforms (grad and curl) operations.

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