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Website of ESTs analysis pipeline for SSRs marker

COE2013-04. Department of Computer Engineering. Website of ESTs analysis pipeline for SSRs marker. Dev eloper. N atthawut Prawalpatamakul ID 533040712-0 N opsompong Nilchan ID 533040718-8. Ad viser. Dr. Jiradej Ponsawat. Co -Adviser. Assist.Prof.Dr . Kanda Runapongsa Saikaew

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Website of ESTs analysis pipeline for SSRs marker

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  1. COE2013-04 Department of Computer Engineering Website of ESTsanalysis pipeline for SSRsmarker Developer NatthawutPrawalpatamakulID 533040712-0 NopsompongNilchan ID 533040718-8 Adviser Dr. JiradejPonsawat Co-Adviser Assist.Prof.Dr. Kanda RunapongsaSaikaew Dr. TatpongKatanyukul

  2. Project Report No.COE2013-04 Agenda 1 • Background and Significance • Objectives • Related work • Design • Development • Results • Problems and Solutions • Conclusion

  3. Project Report No.COE2013-04 Background and Significance 2

  4. Project Report No.COE2013-04 Objectives 3 • To reduce command line procedure by automated system • To manage user authentication • To present analyzed results on website • To notification via email

  5. Project Report No.COE2013-04 Related work 4 Table1 : Related work

  6. Project Report No.COE2013-04 Design

  7. Project Report No.COE2013-04 Website components 5 Index Figure1 : Website components Contact Admin Login Register Download Detail User page Step7 Step6 Step2 Step1 Step3 Step4 Step5

  8. Project Report No.COE2013-04 Folders Structure 6 pipeline usr bin • • • Usr1 Usr2 AnalysisScripts est7_primer.sh est7_primer.sh est7_primer.sh est7_primer.sh est7_primer.sh est7_primer.sh est7_primer.sh • • • Usr1 work1 Usr1 work2 Figure2 : Folders structure

  9. Project Report No.COE2013-04 Check Running Jobs 7 Start Figure3 : Check job flowchart Check Running Jobs From Database YES < Running Max Jobs Jobs Start New Jobs NO Update Database End

  10. Project Report No.COE2013-04 Start New Jobs 8 Start Get Waiting Jobs from Database Start New Jobs Change status from ‘waiting’ to ‘running’ Keep process id(pid) into Database Change status to ‘done’ When job has done End Figure4 : Start job flowchart

  11. Project Report No.COE2013-04 Development

  12. Project Report No.COE2013-04 Tools 9 WEB INTERFACE DATABASE PROGRAMMING SERVER

  13. Project Report No.COE2013-04 EST Analysis Pipeline 10 Figure5 : EST Analysis Pipeline

  14. Project Report No.COE2013-04 Results

  15. Project Report No.COE2013-04 Index Page 11

  16. Project Report No.COE2013-04 Register and Contact Page 12

  17. Project Report No.COE2013-04 User Page 13

  18. Project Report No.COE2013-04 User Page 14

  19. Project Report No.COE2013-04 Upload Page 15

  20. Project Report No.COE2013-04 Parameters Setting 16

  21. Project Report No.COE2013-04 Step 1 Format 17

  22. Project Report No.COE2013-04 Step 2 Length and %N 18

  23. Project Report No.COE2013-04 Step 3 Vector removal 19

  24. Project Report No.COE2013-04 Step 4 Low complexity masking 20

  25. Project Report No.COE2013-04 Step 5 Clustering 21

  26. Project Report No.COE2013-04 Step 6 SSR Detection (1/3) 22

  27. Project Report No.COE2013-04 Step 6 SSR Detection (2/3) 23

  28. Project Report No.COE2013-04 Step 6 SSR Detection (3/3) 24

  29. Project Report No.COE2013-04 Step 7 Primer 25

  30. Project Report No.COE2013-04 Notification Email 26

  31. Project Report No.COE2013-04 Problem and Solution

  32. Project Report No.COE2013-04 Problem and Solution (1/2) 27 • User files and folders permission in linux server • Linux server • Permission : Read / Write / Execute • Support the script that effect on • Security issues

  33. Project Report No.COE2013-04 Problem and Solution (2/2) 28 2. Use “crontab” for execute scripts • Define environment variables defective • Scripts execute with error • Have to modified scripts

  34. Project Report No.COE2013-04 Conclusion 29 • Website available on the server • User can upload file to analyze • User can view the results on website • Done all objective

  35. Questions and Answers

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