Method and a system for automating the execution of AMoRe over a heterogenous network of computers

• US 20040215398A1
• Filed: 10/11/2002
• Published: 10/28/2004
• Est. Priority Date: 10/11/2001
• Status: Active Grant

• Current Assignee: Emerald BioStructures, Inc. (Beryllium LLC)
• Original Assignee: Emerald BioStructures, Inc. (Beryllium LLC)
• Inventors: Mixon, Mark B., Prasad, Sridhar, Feese, Michael, Stewart, Lance J.
• Granted Patent: US 7,203,683 B2
• Time in Patent Office: Days
• US Class Current: 702/19
• CPC Class Codes: G16B 15/00 ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
• CPC Class Codes: G16B 15/30 Drug targeting using structural data; Docking or binding prediction
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: Y10S 707/99945 Object-oriented database structure processing

Abstract

This invention encompasses an apparatus for creating a database containing the results of distributed molecular replacement searches, which comprise data input system for inputting the results of distributed molecular replacement searches and related information and a database generator coupled to said data input system for receiving the results of distributed molecular replacement searches and related information and creating a database for storing the results of distributed molecular replacement searches and related information. The invention includes method of managing the invention of distributed molecular replacement searches.

Claims

1. An apparatus for creating a database containing the results of distributed molecular replacement searches, said apparatus comprising:

a. Data input system for inputting the results of distributed molecular replacement searches and related information.

b. Database generator coupled to said data input system for receiving the results of distributed molecular replacement searches and related information and creating a database for storing the results of distributed molecular replacement searches and related information.

2. The apparatus claimed in claim 1 wherein said data input system includes a display for displaying the data as pictographs on the display.

3. The apparatus claimed in claim 1 wherein said data generator includes a programmed data processor for processing the results of distributed molecular replacement searches and other information, and a storage system for storing the results of said processing.

4. The apparatus claimed in claim 3 wherein said programmed data processor includes a program having a plurality of database managers.

5. The apparatus claimed in claim 4 wherein said plurality of database managers include a user manager for managing information relating to users associated with a distributed molecular replacement search.

6. The apparatus claimed in claim 4 wherein the user manager includes a new user manager to add new users or update existing users associated with a distributed molecular replacement search.

7. The apparatus claimed in claim 4 wherein said plurality of database managers include a project manager for managing information related to a project.

8. The apparatus claimed in claim 7 wherein the project manager includes a new project manager for capturing information relating to a new project

9. The apparatus claimed in claim 4 wherein said plurality of database managers include a computer host manager for managing information related to the computers included in a heterogeneous computing cluster.

10. The apparatus claimed in claim 4 wherein said plurality of database managers include a model manager for managing information related to search models used in a distributed molecular replacement search.

11. The apparatus claimed in claim 4 wherein said plurality of database managers include a reflection manager for managing information related to structure factor data used in a distributed molecular replacement search.

12. The apparatus claimed in claim 4 wherein said plurality of database managers include a run manager for managing information related to execution of distributed molecular replacement searches.

13. The apparatus claimed in claim 12 wherein the run manager includes a reflection queue manager for managing reflections to be used in the execution of a distributed molecular replacement search.

14. The apparatus claimed in claim 12 wherein the run manager includes a command file queue manager for managing files required for the execution of a distributed molecular replacement search.

15. The apparatus claimed in claim 14 wherein the command file queue manager includes a command file builder that manages information used to create files required for the execution of a distributed molecular replacement search.

16. The apparatus claimed in claim 15 wherein the command file builder can select from a group of file types used to setup the distributed molecular replacement routines including reformatting the reflection data, generating and tabulating the structure factors from a search model in a P1 cell, rotation search, translation search, and rigid-body refinement.

17. The apparatus claimed in claim 4 wherein said plurality of database managers include a model queue manager for managing information related to search model queues used in a distributed molecular replacement search.

18. The apparatus claimed in claim 17 wherein the model queue manager includes a model queue generator for associating structural models with a search model queue.

19. A method implemented by computer for creating a database of distributed molecular replacement searches and related information, said method comprising:

a. Receiving via a window, data used to configure files necessary for the execution of distributed molecular replacement programs, said execution data including information identifying the reflection data set, search model queues, model fragment size to be used in the distributed molecular replacement search and whether the solutions generated by the distributed molecular replacement search should be ranked according to the Patterson correlation coefficient or the structure factor correlation coefficient.

b. Storing said received execution data in a database.

20. The method claimed in claim 19, further comprising:

a. Receiving via a file, output from a distributed molecular replacement search, said output including solution angles alpha beta and gamma, solution coordinates x, y and z, the structure factor correlation coefficient for a solution, the R-factor calculated between the search model and reflection data for a solution, and the intensity correlation coefficient for a solution.

b. Storing said received output data in a database.

21. The method claimed in claim 19, further comprising:

a. Receiving via a window, computer host information, said data including computer host network name and computer host network IP address.

b. Storing said received computer host data in a database.

22. The method claimed in claim 19, further comprising:

a. Receiving via a window, reflection data, said data including unit cell parameters and file name.

b. Receiving via a file, reflection data, said data including reflection indices, and structure factors.

c. Storing said received reflection data in a database.

23. The method claimed in claim 19, further comprising:

a. Receiving via a file, search model data, said data including x, y and z coordinates.

b. Storing said received model data in a database.

24. The method claimed in claim 19, further comprising:

a. Receiving via a window, command file queue data, said data including the execution order for the distributed molecular replacement functions.

b. Storing said received command file queue data in a database.

25. A computer readable medium having a plurality of computer executable database managers for creating a database of the results of distributed molecular replacement searches and related information, said executable database manager including:

a. A run manager for entering into the database information on the execution of a distributed molecular replacement search.

26. The computer readable medium of claim 25, further comprising:

a. A computer host manager for entering into the database computer host information.

27. The computer readable medium of claim 25, further comprising:

a. A solution manager for entering into the database distributed molecular replacement solution information.

28. The computer readable medium of claim 25, further comprising:

a. A command file queue manager for entering into the database command file queue information, and

b. A command file manager for entering into the database command file information.

29. The computer readable medium of claim 25, further comprising:

a. A reflection file manager for entering into the database reflection information.

30. The computer readable medium of claim 25, further comprising:

a. A model queue manager for entering search model queue information, and

b. A model file manager for entering into the database search model information.

31. A computer readable medium having stored thereon a distributed molecular replacement results data structure including at least the following fields:

a. Command queue ID field.

32. The computer readable medium of claim 31, further including the following field:

a. Distributed molecular replacement search solution ID field.

33. The computer readable medium of claim 31, further including the following field:

a. Model queue ID field.

34. A method for managing the execution of distributed molecular replacement searches over a heterogeneous network of computers, said method including:

a. Configuring a computer cluster such that there is one master computer and a plurality of remote slave computers.

35. The method claimed in claim 34, further comprising:

a. Initialization of a computer cluster.

36. The method claimed in claim 34, further comprising:

a. Loading reflection data information from the database into master computer memory.

37. The method claimed in claim 34, further comprising:

a. Generating and loading a search model queue information from the database into the master computer memory.

38. The method claimed in claim 34, further comprising:

a. Expanding the search model queue to include a queue of search model fragments if requested.

39. The method claimed in claim 34, further comprising:

a. Notifying an available remote computer host in the computer cluster of the reflection data, search model or search model fragment, command queue, and run parameters required for execution of a distributed molecular replacement search.

40. The method claimed in claim 34, further comprising:

a. Executing the distributed molecular replacement search at the remote slave host.

41. The method claimed in claim 34, further comprising:

a. Filtering distributed molecular replacement output files for solutions.

42. The method claimed in claim 34, further comprising:

a. Scoring the solutions at the remote host for the presence of a distributed molecular replacement solution.

43. The method claimed in claim 34, further comprising:

a. Loading the solutions into the database.

44. The method claimed in claim 34, further comprising:

a. Listening for a response from a remote host indicating that a distributed molecular replacement search has been completed and that the host is available for another distributed molecular replacement search.

b. Repeating 39-44 until the search model queue is completed.