IC Bioinfs/Project1/Existing

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There are a number of different Computational Tools listed on OWW. A number of the examples in Vincent's list-o-links can be found from this page.

One particularly interesting bit of software is BioJADE, which is a design tool which connects to the registry of parts. It's far more ambitious than what we are trying to produce- it's a design tool, database interface and mathematical modelling package all baked into the same doughnut. Useful to us is the schema for the parts registry is given in the user guide, both graphically in figure 3.1 and in SQL in the appendix at the end.

GenoCAD and Tinker are again design & modelling tools, appears to be designed with ease-of-use as a priority. GenoCAD allows you to choose from a number of libraries, including BioBricks, in the construction of your system. I'm not sure if it references the Registry live or has a database of its own. The goals of Tinker include extension to external databases, but it's not there yet (from what I gather).

All three tools visualise layers of emergent properties- DNA code under genes under systems displayed like an electrical schematic.

BrickIt and the Berkley Registry are more what we're after. From what I've seen of the MIT Registry of Parts it's difficult to properly filter your results- you can end up scrolling hopelessly through a long list of parts filtered by one characteristic. JBEIR allows you to add multiple filters before running a search, though the available filters are in my opinion less intuitive than MIT's classification. The Berkley registry also allows BLAST searches, which is very useful (or will be once they have more than 19 parts).

I've seen no more of BrickIt than anyone else- it's currently very slowly downloading, alongside some supporting software, so I can give it a try. The interface looks very good. It is explicitly a local tool, which is where its aims differ from ours.

None of the above use the dastardly DAS. The tool CARGO does. It is a web-based application which uses DAS and a couple of other methods to simultaneously scan a number of different databases for information on a given gene- select a cancer (given some filter) and then watch as the info loads up! My experience was that most widgets returned no information and beyond that I didn't find the filters very friendly, but I don't know what to look for. In any case, the CARGO release notes might be useful, though they aren't very technical. Genoviz is (as is obvious from the name) a genotype visualisation tool which implements DAS, and I think was mentioned somewhere on the BioDAS site as a good example to learn from.