Ian Yen Lee

1
Ian Yen Lee(???)

• Situation of Ongoing Project and Life in China
• Computer Network Information Center,Chinese
  Academy of Sciences 
• Beijing, China
• July 13, 2005

2
Project Basics

• Goal To discover extent of the ability to
  determine evolutionary relationships accurately
  based on partial domain content though fold
  verification at a certain percentage
• This should to be achieved by using SAM, to match
  HMM models to protein sequences. With these
  results Phylip can be used to construct an
  evolutionary tree

3
Progress

• Week 1, (6/27-6/29) (1st couple days in lab)
• Got familiar with the lab
• Resolved technical difficulties with internet and
  software with provided terminal
• Uploaded archives to Deepcomp
• Began fragmenting program to pick out proteins in
  genomes

4
Progress cont

• Week 1-2 (6/29-7/9) (?? Changchun)
• Attended lectures on Computational Methods in
  Bioinformatics
• Attended International Bioinformatics Workshop
• Detoured to Harbin for 2 wonderful days
• Week 3 (7/10-7/15)
• Technical difficulties with memory limits in
  DeepComp resolved
• Began examining SAM and how to use it
• Configured some files
• Reading documentation on SAM and the script for
  Superfamily
• Reviewed C programming
• Installed Nonredundant Protein Database and
  WU-Blast

5
Progress cont

• Weekend 4 (7/16-7/17) (Great Wall)
• Climbed to the highest point of the Great Wall
• Got blessed by a monk over 100 years of age
• Side tripped to the 13 Ming Tombs site
• Week 4 (7/18-7/21)
• Completed fragmenting program
• Got SAM running, currently running first 2
  partial genomes on DeepComp
• Failed for some reason last night, currently
  investigating
• Began examining Phylip and how to use it

6
What needs to be done

• Week 4 (7/22)
• Examine Phylip and discover input format
• Week 5 (7/25-7/29)
• Gauge the number that can be done
• Begin and hopefully implement program to convert
  SAM results to input into Phylip
• Week 6 and on
• Consider running SAM continuously, using Phylip
  less or after return

7
Recent Experiences

• Peter and Gabriele visited, providing us with the
  opportunity to go to Wangfujing (???), a famous
  teahouse, and the Forbidden City
• Went to the Great Wall of China
• Visited Xidan (??) for some shopping
• Played lots of basketball with my team
• This weekend we plan to go to the Summer Palace
  with special interest in rowing on the lake
  inside

8
The Garden in the Forbidden City
The famous tea house with classical Chinese style
performances
Thanks for the visit!
9
The Great Wall!