Students' Learning Experience and Feedback

1.Thanks for all the help throughout this period!By doing this project, I'd gained much knowledge about Burkholderia pseudomallei and the Bioinformatics databases and software, and I really enjoyed doing this project, though I had a problem managing my time. .I would like to thank Prof Tan Tin Wee for his comprehensive lecture notes and explanation on Sequence Comparison and Algorithms, Sequence alignments, introduction to PAM, BLOSUM, FASTA and BLAST Programs. Moreover, his continuous encouragement has driven me into seeking as accurate a result as I can. I would also like to thank Prof Vladimir Brusic for his precise lectures on Biological Databases and Bioinformatics software. These lectures enable the project to be carried out with greater ease and efficiency. Thanks a lot!

2. I felt that the project was a good way to give us some experience into bioinformatics as it is a research tool, more than anything else to us biologists. Wonder if we could have more practicals in the curriculum so that we could pick up Linux? I found that a great advantage actually, when doing all the searches and all that--Windows takes a very long time to load all the text documents and this is not the case in Linux--in any case, bioinformatics projects are always data- intensive, another reason why doing it on Windows, while sufficient for school projects, may not be a good way to do it in a real research settings, besides the fact that I understand most computer labs doing bioinformatics are Unix/Linux based. However I understand that with HTML to learn, most may feel a bit overwhelmed with the amount of computing stuffs if they have to pick up Linux as well. Enjoyed the lectures on algorithms and wished there could be more of such in the NUS curriculum to give us more of an idea into the multidisciplinary nature of bioinformatics. Just some feedback on my part--overall I think this is a really good way to force us to think critically about minor and sometimes neglected issues like the type of matrices used to calculate sequence alignments and was quite an eye opener.

3. In the process of carrying out this ordeal task unveiling the genes and identifying their functions, I would like to take this opportunity to thank my lab partner , Goh Meiling who collaborated with me in identifying the flagellar pathway as well in obtaining the MSA results and the dendogram. She has been a tremendous partner to work with as her previous knowledge of microbiology more than overwhelmed me in assisting me in my findings and indirectly my conclusions. On top of that, my appreciation also goes to the TA, Mr Justin for his dedication in his conscientious effort to rectify my lack-of-knowledge understanding of the project in one way or another. At the same, Dr Tan also deserves his credit for being overzealous in his effort and inspiring up till to the last day of project submission. In my personal opinion, this project not only allows, us, students benefit of utilizing the tools of bioinformatics but more importantly, it provides the insight of the endless possibilities with what we can do through bioinformatics. Bioinformatic tools is a saviour for humanity all the way from identifying genes to understanding how virulent bacterium works which in turn equates to saving lives.

5. Due to the limited time and limited bioinformatics and biochemistry knowledge, I must stop my mini-project now. Here I want to show my sincere appreciation to my dearest Supervisor, Dr. Tan Tin Wee. Without their help, I cannot finish my mini-project in such a short time. In the future, I'll try my best to learn more about bioinformatics from them. If luckily enough, I may have the chance to put in more energy in bioinformatics research of the genes of biological pathways of Burkholderia pseudomallei.

6. I would like to thank A/Prof Tan Tin Wee for helping me with analysing the data and giving me advices when I needed it most. Also, not forgetting Justin and Bhuvana, for imparting the most needed technical skills that is required for the completion of this mini-project. And lastly, my classmates for sharing their valuable advice and ideas in the course of preparing this report. Thank you!

7. Here I would like to thank the following people who have helped me in my mini project that really dained out! Prof Tan Tin Wee, for his lectures and explanations during the practical sessions. Justin, for so kind to answer all my questions in class and in emails. Bhuvana, for explaining during practical and all my fellow classmates who had helped me through the mini project!

11. I would like to express my gratitude to the T.As in my group whom have been patient and helped to clarify our doubts whenever we have difficulties with the project.I would also like to thank my friend, Dave, who has generously let me use his computer to do research when my computer has problems.

12. I would like to express my thanks to Dr Tan Tin Wee and to my teaching assistants, Mr. Justin Choo and Miss Bhuvaneswari, who have taught me all the various methodologies in doing this mini-project. Also, I wish to express my gratitude to friends who have helped me with this project especially Karen, because she has been a great help to me. I would also like to thank Daniel for helping me to upload my project.

13. I would like to thank Dr. Tan Tin Wee for his guidance and help in the process of the creation of this website, without whom the successful completion of this project would have been impossible. I would also like to thank my teaching assistants, Mr Justin Choo and Ms Narasa Ramaswamy Bhuvaneswari for their advice too

14. I would like to acknowledge A/P Tan Tin Wee for providing his help and valuable advises in this Mini-project. And not to forget my Teaching Assistances (especially to Mr. Chen Xin and Ms. Yun Ping) for their patience in answering all of my HTML and Mini-project questions.

16. I would like to thank my TAs, Chen Xin and Lim Yunping, for their invaluable advice especially pertaining to the methodology proposed in my project

17. I would like to thank Prof Tan Tin Wee, my TAs Mr Chen Xin and Ms Lim Yun Ping, for the opportunity to embark on this interesting project and the instructions and assistance they had kindly given us during the course of this research.

18. This work was accomplished with the guidance of Chen Xin and Lim Yun Ping from the National University of Singapore. I thank them for their kind support.

19. I like to thank all the Professors, various TAs ,lab technicians and my friends in this course who has spend their valuable time for extending their helping hands in guiding me throughout this practical. Thank You!

20. I would like to thank A/Prof Tan Tin Wee for his interesting and informative lectures and kind guidance, teaching assistants, Mr. Chen Xin and Ms. Lim Yun Ping for their patience, assistance and guidance throughout the entire duration of this project

21. Special thanks to Dr. Tan Tin Wee, Mr. Chen Xin, and Ms. Lim Yun Ping for their patience and guidance throughout the process of completing this project.

22. I would like to express my thanks to Dr. Tan Tin Wee, Cao Zhiwei and Manisha for their guidance on creating and uploading of the web pages. I would also like to thank all of my friends who had helped me in the process of doing this project. Thank you for all your valuable ideas

23. I would sincerely like to thank A/P Tan Tin Wee for his time and kind explanation that had enlightened me on various aspects of this project, as well as Ms Cao Zhiwei for being a patient and responsible TA.

24. After carrying out these steps, I have successfully located the locus of 18 genes in Burkholderia pseudomallei. I realize that it is difficult to identify unknown genes loci in the genome of an organism through Blasting. For example, identifying unknown enzyme-genes in B.pseudomallei in step 3. I had tried my best to search for supporting material for the existence of the genes in Burkholderia pseudomallei but some related journals are published to restricted access area. For example, I could not get the journal on research of Quorum Sensing genes in Burkholderla Pseudomallei and published to Siriraj Medical Library in August 2002 by Putthapoom Lumjiaktase.Databases and online tools such as Blast, ClustalW, Similarity Searches and Extractseq introduced in this project as well as this module, are indeed very useful. Databases together with Bioinformatics tools are used for analysis of biological data and biological systems. They are also used for simulation of laboratory experiments and predictions that lead to the design of experiments.There are still many known Burkholderia pseudomallei genes in the databases waiting to be identified the location in its genome. This could be my future work for this project.Finally, I would like to end my work here. I would like to thank Professor Tan Tin Wee for giving us the opportunity and teaching us the essential knowledge to carry out this meaningful mini project. I also want to thank my tutors for giving guidance and suggestions in doing this project.

25. I'd like to thank our lecturers, Dr Shoba Ranganathan and Dr Vladmir Brusic, for providing the necessary foundation for this module and excellent coverage of useful bioinformatics tools. I'd also like to thank our invaluable TAs, Justin and Bhuvana for their patience and assistance. Without them, the project could not have been carried out smoothly. Lastly, special thanks to Dr Tan Tin Wee for imparting valuable knowledge on the use of essential bioinformatics tools and the chance to apply these knowledge to good use. And finally, I deeply appreciate Dr Tan's helpfulness throughout the entire course of our project.

26. I wish to thank A/Prof Tan Tin Wee for giving me a chance to have a real-world hands-on experience in genome annotation.Also, I would like to express my gratitude to Ms Cao Zhiwei and Ms Manisha Brahmachary for answering my queries whenever they arise.

27. After the entire data annotation, I have experience what it is like to be involved in Bio-informatics research. I would like to further on the research by exploring PDB but due to the lack of knowledge of the RASmol programme and the nature of the site, this research was stopped here. I would like to thank our group C T.As, Munisha and Zhiwei for their kind help and patience, not forgetting Prof Tan who also contributed by giving valuable advices.

28. Thanks for all of you that make this module enjoyable.