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Autobiography
- Currently a senior studying bioengineering at the UCB, I was born on April 12, 1988 in the humble city of San Jose. After two weeks, my family settled down in Fremont, CA, just twenty minutes away. I grew up enjoying Chinese culture, playing Super Mario, riding my bike in the neighborhood culdesac, and assembling wooden models, Legos, Kenix, and anything I could get my hands on--that is probably why I eventually choose to ditch my naive dream of being a doctor and pursue engineering. Computational biology was never of particular interest of mine until I stumble upon the grand world of computer science.
My Links
- WelcomeGuest to learn TWiki
- Sandbox web to try out TWiki
- AndrewHuSandbox? just for me
- Cello J, Paul AV, Wimmer E. Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template. Science. 2002 Aug 9;297(5583):1016-8. Epub 2002 Jul 11.
- Polio vaccine (Wikipedia)
- An Interesting Link about Polio: Burton A, Monasch R, Lautenbach B, Gacic-Dobo M, Neill M, Karimov R, Wolfson L, Jones G, Birmingham M. WHO and UNICEF estimates of national infant immunization coverage: methods and processes. Bull World Health Organ. 2009 Jul;87(7):535-41.
Homework
Why is Computational Biology related to Synthetic Biology?
- Much of synthetic biology is related to the kinetics of reactions, namely signal cascades, transcription of RNA, protein synthesis, etc, computational biology allows for a model/simulation of these reactions given initial values.
- Simply to compile, organize, and analyze data from synthetic biology, computational biology aspects such as computer science and statistics are increasingly necessary.
What is the Difference Between a Virus and a Transposon?
- A virus is a "biological hacker" or parasite that uses cell lines of an organism as its hosts. Therefore the same virus can infect multiple cells of an organism. In contrast, a transposon stays within one cell, and only affect that one cell, and its daughter cells.
- Technological Application of transposon include directed mutagenesis to mute specific gene expression, while viruses have been used to synthesize semiconductors and of course as vectors for gene therapy.
- Limitations to Modified Transposons and Viruses
Problem 6
| Tools | Examples |
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| 1. Protein Structure Prediction | Ab initio protein structure prediction software is a software tool using first principles of chemistry and physics to predict the tertiary structure of protein by its primary structure or linear sequence. Some prominent examples include ROBETTA, Abalone, and CABS. Comparative protein structure modeling software is another software tool. But it uses large databases of previously-found protein structures to predict the unknown protein structure by comparing the known sequences' sequences to the unknown protein's sequence. Three examples include MODELLER and Biskit and SWISS-MODEL. |
| 2. Gene Function | Controlled vocabularies for gene/enzyme function, i.e. the Gene Ontology, is a database that uses three organizing principles: cellular components, biological process, and molecular function, to help biologists find information that might be named differently by other scientists. Similarly, Biochemical pathway databases have loads of biology information, but is primarily concerned with signal cascades, metabolic pathways, and enzymes reactions. A popular tool examples are ExPASy and BioCarta and BRENDA. |
| 3. Structure Analysis | Protein/protein docking software is useful to finding the nature of interactions between interacting proteins, their spatial configuration, and the strength and specificity of the interactions. Rosetta and Discovery Studio Protein Modeling and Sequence Analysis Software are examples of two. Meanwhile Protein/small-molecule docking software visualizes protein to small-molecule interactions sometimes called docking, which includes inhibitors to an enzyme, ligand to receptors, drugs to target proteins, etc, to elucidate biological phenomena. Some examples include Situs and Flexible Molecular Docking Module. |
| 4. Sequence Analysis | Sequence assembly software, i.e. SeqAssem and DNA BASER Assembler, allows one to view and edit DNA sequences and detect mutations and align interested sequences by homology. Gene-finding software more specifically identifies gene structures, introns and exons, in genomic DNA; some software include Genescan, GeneMark, and GeneFinder. |
| 5. RNA Structure | RNA folding software includes a group of programs that use models, thermodynamics, kinetics, statistics, and other programming algorithms, to predict RNA folding, RNA secondary structures, hybridization and melting patterns. Examples are RNAfold and RNAshapes. RNA design software has the capacity to design RNA from predefined structures while checking for its off-targets, scoring its performance, and finding its secondary structure. AsiDesigner and Vienna RNA Package are two RNA design software. |
Related topics
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