"TIGP Bioinformatics Program Orientation - PowerPoint"
TIGP Bioinformatics Program Orientation Wen-Lian Hsu 許聞廉 Institute of Information Science Academia Sinica 2010/2/17 1/52 Division of Life Sciences Institute of Plant and Microbial Biology Institute of Biomedical Sciences Institute of Cellular and Organismic Biology Agricultural Biotechnology Research Center Institute of Biological Chemistry Genomics Research Center Institute of Molecular Biology Biodiversity Research Center 2010/2/17 2/20 The Genomics Research Center (GRC) in Academia Sinica Organization Incubation Center Core facilities 2010/2/17 3/20 Organization 2010/2/17 4/20 Incubation Center 2010/2/17 5/20 Core Facilities ENU Mutagenesis and Genotyping Facility High Throughput and High Capacity Facilities for Proteomic Research, Service and Technology Development High Throughput Protein X-ray Crystallography Core High Throughput Recombinant Protein Production Core Laboratory High-Field Biomacromolecular Solution NMR Core Facility Functional and Micro-Magnetic Resonance Imaging Center Clinical core for Genomic Medicine Research Establishing a High-throughput Genotyping Core Lab Bioinformatics: Computing Cluster and Applications Computer Science Algorithm design (knowledge based ) Programming, software development Prediction (exon, intron, protein structure) Natural language processing Literature search Biological knowledge base construction Machine learning Information management 2010/2/17 7/20 Statistics Clustering Classification Probability Hidden Markov Model Bayesian network Various machine learning models Data mining Inference Hypothesis testing 2010/2/17 8/20 BP - Cooperating Universities National Yang Ming University National Chiao Tung University Nation Tsing Hwa Univeristy Within Academia Sinica Institute of Information Science Institute of Biomedical Sciences Institute of Statistical Science 2010/2/17 9/20 Bioinformatics Program in Academia Sinica Four Research areas: Computational biology Biological knowledge management Bioinformatics applications Computational structural biology We emphasize the study of computational techniques that can speed up biological problem solving or renovate biological experiments. Find your advisor after one year among core faculty members 2010/2/17 10/20 Course Program Required: 1 year tutorial reading, lab rotation; 2 year Seminar CORE courses: You can waive a course, but still need to take the exams of the course, unless approved by the academic committee. B1. Biology I B2. Biology II C1. Computing I (algorithms) C2. Computing II (statistics) C3. Advanced algorithms (machine learning) Electives: B3. Computational Genomics and Systems Biology C4. Advanced statistics 2010/2/17 11/20 Qualifying Exam (written) Content B1, B2, C1, C2, C3 Need to finish all tests before the end of the 3rd year: Each year, the exam is offered at the start of the second semester The test for each course can be taken at most twice and the better of the two grades will be counted into the total. In the end, you pass if can get a grade ≧ 60% of the total grade. This has been agreed upon for all collaborating universities 2010/2/17 12/20 Admission to Candidacy (within 3 years) Pass the qualifying exam Pass the proposal exam 2010/2/17 13/20 Degree Requirement Get a TOEFL score of at least 100 IBT score (or equivalent) for non-native speakers (the sooner the better) Publish at least two first-author papers in leading bioinformatics journals or conferences to be approved by the committee Write a thesis Successful defense of your thesis 2010/2/17 14/20 Miscellaneous (I) Use English in academic-related discussion Stipend provided for 3 years Afterwards, the student needs to find support from advisors or other sources Poor academic performance could result in stipend reduction Be prepared for Interdisciplinary training Always study hard before you go to a class (try to memorize the vocabulary beforehand) Go to as many seminars and presentations as you can 2010/2/17 15/20 Miscellaneous (II) Course presentations will be taped in computer so they can later be reviewed You may consult previous years’ material Every student needs to be a TA for one semester 1 year Chinese course Advanced English course International conference presentations encouraged and supported once No more than 7 years of study 2010/2/17 16/20 Academic Honesty & Plagiarism (I) plagiarism, i.e., the failure to properly acknowledge the use of another person's work Submission for assessment of material that is not the student's own work Misrepresentation of a piece of group work as the student's own individual work Collusion, i.e., obtaining assistance in doing work which is meant to be solely the student's own work 2010/2/17 17/20 Academic Honesty & Plagiarism (II) The sanctions may range from: ���� A zero on the coursework in question ���� A reduction in the overall mark ���� A grade of F for the whole course 2010/2/17 18/20 Four Research Areas (I) (1) Computational biology: Design various algorithms for sequence analysis, gene prediction, disease gene mapping, motif finding, and gene networks. (2) Biological knowledge management: The integration of various heterogeneous databases, biological knowledge representation, automation of pipeline experiments, and the construction of various annotation databases. In addition, biological literature search is also a crucial component. 2010/2/17 19/20 Four Research Areas (II) (3) Bioinformatics applications: Using existing tools to analyze biological sequences, microarray data, proteomic data, etc. Statistical analysis and data mining techniques will be used to reach the goal of "information-driven biomedical research." (4) Computational structural biology: Protein structure prediction and classification, automated biomolecule docking, and molecular dynamics. 2010/2/17 20/20 Q&A 2010/2/17 21/20