PathwayAccess. Everybody is using one of many different pathway databases. We need a tool to integrate pathways from different sources. Please cite: PathwayAccess: CellDesigner Plugins for Pathway Databases John L. Van Hemert; Julie A. Dickerson Bioinformatics 2010; doi: 10.1093/bioinformatics/btq423 NEW! PathwayAccess plugins now use XML to store rich datasource-specific annotation, integrate based on synonyms, and even visualize integration results! Introduction PathwayAccess is a suite of CellDesigner plugins which directly interact with pathway datasources so that the user can accomplish one or both of the following: download and integrate one or more pathways to a CellDesigner modelupload (or commit) a CellDesigner model to a datasource.
The dataflow diagram for typical use of the PathwayAccess plugins: Notice how the dataflow arrows can one or both directions, depending on functionality supported by the datasource, api, and plugin. Notes about PathwayAccess compatability with CellDesigner versions: Solve for X: Juan Enriquez on harnessing synthetic genetics. BBCU - Sequence Analysis/Promoters. Creating Cell Parts from Scratch. Researchers at Harvard University have built a functional ribosome–the cell’s protein-making machine–from scratch, molecule by molecule. The creation represents a significant step toward making artificial life, and it could ultimately fill a major gap in our understanding of the origins of life. But the scientists who made the ribosome are most interested in its industrial applications. They plan to genetically tinker with the molecular machinery so that it can make proteins more efficiently, as well as proteins that are the mirror image of those ordinarily found in nature. Both improvements could be a major advantage in the pharmaceutical industry, among others.
To make the ribosomes, George Church, a Harvard geneticist, and postdoctoral researcher Mike Jewett first disassembled ribosomes from Escherichia coli, a common lab bacterium, into its component molecules. Next, the researchers want to create a ribosome that can re-create itself. Gene Sequencing for the Masses. An inexpensive new gene-sequencing machine is due to hit the market next month, and its creators hope that it will make sequencing more common, ultimately giving a boost to personalized medicine. The machine is the brainchild of George Church, a genomics pioneer who developed the first direct sequencing technology as a graduate student in the 1980s and helped initiate the Human Genome Project soon after. Church sees greater access to sequencing as a vital component in the drive toward personalized medicine, in which treatments and preventative medicine are tailored to an individual’s genetic makeup.
The new machine, which was developed with an “open source” philosophy, was commercialized by Danaher Motion, based in Salem, NH, with the specific intent of keeping costs low. “It seems like the biomedical-instrument field in general tries not to commoditize,” says Church, who heads the Center for Computational Genetics at Harvard Medical School, in Boston.
Lee Cronin: Making matter come alive. High-Speed Evolution Aids Drug Development. By exploiting the rapid replicating power of viruses, researchers were able to make biological molecules in the laboratory evolve much more rapidly than they can with existing approaches. Their new method, called phage-assisted continuous evolution (PACE), could be used to accelerate the development of therapeutic proteins, such as new cancer drugs, or to tackle unsolved questions about how evolution works. Most traditional pharmaceutical agents are small molecules, but a number of promising new therapies are based on macromolecules, such as proteins. So-called “directed evolution” gives scientists a way to adapt a naturally occurring macromolecule to perform a specific therapeutically useful function, such as bind to a cancer-linked protein.
“For some applications, the speed of conventional protein evolution is a bottleneck,” says David Liu, a professor of chemistry and chemical biology at Harvard University and senior author of a paper describing the new technique in Nature.