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.

• Java Applets with provision to zoom and pan.

• 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.

• 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.

• 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.

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