Grid implementation on Basic Local Alignment Search Tool (BLAST) by Berkley Open Infrastructure for Network Computing (BOINC)

Full documentation at our Wiki

Objectives of this project

1. This project aims to setup BOINC system that distributes tasks of BLAST (e.g. query sequences and databases ) to each computer client node within an organization or institute.
2. This project aims to use a "grid computing" mode of BOINC. For, a "volunteer computing" mode please refer to references below.

Prerequisites

1. Several personal computers to serve as clients with:

2. Microsoft Windows as the main operating system (32-bit or 64-bit is OK)

3. Installed with BOINC manager (http://boinc.berkeley.edu/wiki/BOINC_Manager)

4. Full authorization to access each computer during performing BLAST (e.g. during off-hours)

5. One personal computer to serve as the project server with:

6. Installed with Oracle VM VirtualBox (https://www.virtualbox.org/) or other VM software that can run a '.vdi' file.

7. VM image of BOINC server (https://boinc.berkeley.edu/dl/debian-7-boinc-server-140412.7z)

8. Full authorization to access this computer during performing BLAST (i.e. during off-hours)

9. OPTIONAL: Installed with remote administration software (e.g. NetSupport, TeamViewer, BOINCtasks ) for monitoring and controlling clients, and BOINC manager mass deployment.

10. Stable network connections among clients and the server (e.g. Wi-Fi, LAN) with:

11. OPTIONAL: If data protection is required (e.g. analyzing patient sequencing data), the network without a direct Internet connection will be neccesarry.

12. Standalone BLAST application.

13. version 2.2.30 for Microsoft Windows 32-bit is perfered (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/). 1. The later versions do not support Microsoft Windows 32-bit 2. BLAST for Microsoft Windows 32-bit could run on Microsoft Windows 64-bit, but not vice versa.

14. Query sequences for BLAST analysis.

15. A training dataset from the Genome in a Bottle consortium is used as an example here (NA12878)(ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/NA12878/NIST_NA12878_HG001_HiSeq_300x/131219_D00360_005_BH814YADXX/Project_RM8398/Sample_U0a/U0a_CGATGT_L001_R1_001.fastq.gz).

16. Reference database or sequences.

17. hg38 database is used as an example here (http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz).

Further reading

1. Computing with BOINC (https://boinc.berkeley.edu/trac/wiki/ProjectMain)
2. BLAST® Command Line Applications User Manual (http://www.ncbi.nlm.nih.gov/books/NBK279690/)
3. Oracle VM VirtualBox documentation (https://www.virtualbox.org/wiki/Documentation)