System and method for programatic access to biological probe array data

1. A method for enabling a user-provided application to access one or more data structures of a second application, comprising the acts of:

providing at least one applications programming interface comprising one or more code libraries that integrate the second application with the user-provided application, and are callable from the user-provided application to access at least one of the one or more data structures of the second application; and

transferring pixel data, intermediate results data, or both, directly or indirectly from the at least one of the one or more data structures of the second application to the user-provided application, wherein the pixel data comprises one or more emission values generated from one or more detected emission signals from a plurality of probe locations on a probe array, each probe location comprising one or more probe molecules.

2. The method of claim 1 , wherein:

the pixel data includes data from one or more biological experiments.

3. The method of claim 1 , wherein:

the intermediate results data includes data from one or more biological experiments.

4. The method of claim 1 , wherein:

the probe molecules include nucleic acids.

5. The method of claim 1 , wherein:

the probe molecules include peptides or polysaccharides.

6. The method of claim 1 , wherein:

the probe array includes a spotted array.

7. The method of claim 1 , further comprising:

the act of enabling one or more target molecules to interact with one or more probe molecules.

8. The method of claim 7 , wherein:

the one or more target molecules include any one or more of the following biological materials: cells; proteins; genes, EST's, or other DNA sequences; ligand; receptor; peptide; or nucleic acid.

9. The interface of claim 1 , wherein:

the code libraries include executable code callable from the user-provided application.

10. The method of claim 1 , wherein:

the at least one applications programming interface hides the format of one or more data files, wherein the one or more data files comprises the pixel data, the intermediate results data, or both.

11. The method of claim 1 , wherein:

the at least one applications programming interface is downloadable from one or more remote sources.

12. The method of claim 1 , wherein:

the at least one or more code libraries enable export at least one data element to a standardized format.

13. The method of claim 1 , further comprising:

storing the pixel data, the intermediate results data, or both, in one or more data files; and

enabling the user-provided application access to the one or more data files, including providing at least one applications programming interface and employing one or more code libraries to enable transfer of at least one data element directly or indirectly from at least one of the data files to the user-provided application.

14. The method of claim 13 , wherein:

the one or more data files comprises one or more, in any combination, of .DAT-type file, a .CEL-type file, or a .CHP-type file.

15. The method of claim 13 , wherein:

the one or more data files includes a probe array data file.

16. The method of claim 13 , wherein:

the probe array data file includes a .CDF-type file.

17. The method of claim 13 , wherein:

the at least one data element comprises one or more, in any combination, of probe set data, quality control data, probe array name, x, y coordinate data, probe array type data, sample data, hybridization data, scan data, corner feature data, intensity data by probe position, intensity data by line, algorithm parameter data, probe intensity data by index, probe intensity data by position, probe intensity data by index and position, standard deviation data, pixel data, outlier data, masked feature data, background quality control data, header data, probe set data including data by index or all probe sets, statistical results, empirical results, probe pair data including intensity by x, y coordinates, perfect match probes, mismatch probes, background intensity, or quality control data.

18. The method of claim 13 , wherein:

the at least one applications programming interface hides the format of the one or more data files.

19. The method of claim 13 , wherein:

the at least one applications programming interface is downloadable from one or more remote sources.

20. The method of claim 13 , wherein:

the at least one or more code libraries enable export of the at least one data element to a standardized format.

21. The method of claim 20 , wherein:

the standardized format includes a MAGE-ML format.

22. An applications programming interface comprising:

one or more code libraries that integrate a user-provided application with a second application, and are callable from the user-provided application to access at least one of the one or more data structures of the second application;

wherein the code libraries enable transfer of pixel data, intermediate results data, or both, from at least one data structure of the second application directly or indirectly to the user-provided application; and

further wherein the pixel data and intermediate results data includes data from one or more biological experiments, at least one of which comprises an experiment using one or more probe arrays.

23. The interface of claim 22 , wherein:

the code libraries include executable code callable from the user-provided application.

24. The interface of claim 23 , wherein:

the second application comprises one or more server executables that interface between the executable code and the at least one data structure.

25. The interface of claim 24 , wherein:

at least one of the server executables is a COM server.

26. The interface of claim 22 , wherein:

the number of biological experiments is more than one, and

the one or more code libraries are further that enable batch transfer of the pixel data, the intermediate results data, or both, from the more than one biological experiments.

27. The interface of claim 22 , wherein:

the biological experiments include experiments using at least one synthesized array or at least one spotted array.

28. The interface of claim 22 , wherein:

the biological experiments include experiments using at least one synthesized array and at least one spotted array.

29. The interface of claim 22 , wherein:

the at least one data structure is organized according to a database schema.

30. The interface of claim 29 , wherein:

the database schema comprises the AADM schema.

31. The interface of claim 22 , wherein:

the at least one data structure is included in a laboratory information management system.

32. The interface of claim 22 , wherein:

the one or more code libraries hide the format of the one or more data files.

33. The interface of claim 22 , wherein:

the one or more code libraries are downloadable from one or more remote sources.

34. The interface of claim 22 , wherein:

the one or more code libraries enable export of the at least one data element to a standardized format.

35. The interface of claim 22 , wherein:

the user-provided application includes any one or more of the following: a data-mining tool, an image-processing tool, or a data-processing tool.

36. The interface of claim 22 , wherein:

the user-provided application includes a data-processing tool that includes any one or more of the following functions: determining degrees of hybridization, determining absolute expression of genes or EST's, determining differential expression over two or more experiments of genes or EST's, making genotype comparisons, detecting polymorphisms, or detecting mutations.

37. The interface of claim 22 , wherein:

the one or more code libraries comprise one or more high or low level programming languages.

38. The interface of claim 22 , further comprising:

one or more code libraries that enable transfer of pixel data, intermediate results data, or both, from at least one data element from one or more data files directly or indirectly to a user-provided application.

39. The interface of claim 38 , wherein:

the one or more data files comprises one or more, in any combination, of .DAT-type file, a .CEL-type file, or a .CHP-type file.

40. The interface of claim 38 , wherein:

the one or more data files includes a probe array data file.

41. The interface of claim 40 , wherein:

the probe array data file includes a .CDF-type file.

42. The interface of claim 38 , wherein:

the at least one data element comprises one or more, in any combination, of probe set data, quality control data, probe array name, x, y coordinate data, probe array type data, sample data, hybridization data, scan data, corner feature data, intensity data by probe position, intensity data by line, algorithm parameter data, probe intensity data by index, probe intensity data by position, probe intensity data by index and position, standard deviation data, pixel data, outlier data, masked feature data, background quality control data, header data, probe set data including data by index or all probe sets, statistical results, empirical results, probe pair data including intensity by x, y coordinates, perfect match probes, mismatch probes, background intensity, or quality control data.

43. The interface of claim 38 , wherein:

the one or more code libraries hide the format of the one or more data files.

44. The interface of claim 38 , wherein:

the one or more code libraries are downloadable from one or more remote sources.

45. The interface of claim 38 , wherein:

the one or more code libraries enable export of the at least one data element to a standardized format.

46. The interface of claim 45 , wherein:

the standardized format includes a MAGE-ML format.

47. The interface of claim 38 , wherein:

the user-provided application includes any one or more of the following: a data-mining tool, an image-processing tool, or a data-processing tool.

48. The interface of claim 38 , wherein

the user-provided application includes a data-processing tool that includes any one or more of the following functions: determining degrees of hybridization, determining absolute expression of genes or EST's, determining differential expression over two or more experiments of genes or EST's, making genotype comparisons, detecting polymorphisms, or detecting mutations.

49. The interface of claim 38 , wherein:

the one or more code libraries comprise one or more high or low level programming languages.