Endy:Notebook/Wetware IDE

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Project Description

 * We are in pursuit of an integrated development environment (IDE) that supports review, design, and implemention of standard biological parts
 * Our core goals are to develop programming languages, information models, communication/computational architectures that support the development and responsible use of standard biological parts.

Existing Software Tools

 * Synthetic Biology
 * Clotho, Registry of Standard Biological Parts, Gene Designer, GenoCAD, Athena, BrickIt, GeneJax, BioJADE, PoBoL, SynbioSS
 * Systems Biology
 * Systems Biology Workbench,SimBiology, BioSPICE,CellDesigner,Cytoscape,  xCellerator,Cellerator
 * Molecular Biology
 * NUPACK,BioCocoa,ApE,EnzymeX,Four Peaks,Genome Browser,CLC Genomics Workbench,MacGDE,CLC DNA WorkbenchCLC Protein Workbench,CLC RNA Workbench,CLC Sequence Viewer,KoriBlast,Geneious,MacVector,Novocraft aligner package for the Illumina Genome Analyzer,Mac Sequence,Molecular Viewer,AlleleID,Designer,PrimerPlex,OligoChecker X,PhyloCoco,OligoFaktory,GelEval,Serial Cloner,Central Dogma,OnScreen DNA Lite,A/G BLAST
 * Software Engineering IDE
 * Apple Xcode, Microsoft Visual Studio, Eclipse

Peer-Reviewed Literature

 * Czar MJ, et al. Gene synthesis demystified. Trends in Biotechnology 27(2):63-72. (2009) Link
 * Goler JA, et al. Genetic design: rising above the sequence. Trends in Biotechnology 26(10):538-44. (2008) Link
 * Peccoud J, et al. Targeted development of registries of biological parts PLoS ONE 3(7):e2671. (2008) Link
 * Cai, et al. A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts. Bioinformatics 23(20): 2760-2767. (2007) Link
 * Villalobos, et al. Gene Designer: a synthetic biology tool for constructing artificial DNA segments. BMC Bioinformatics 2006 7:285. Link

Use Cases/Requirements

 * Physical building of standard biological parts.
 * primers design for part cloning (including prefix and suffix. see:Ginkgo)
 * primers design for mutagenize the restriction sites present in the original sequence to fit to the BBS designed one. A very good program here: stratagene
 * Classical DNA/RNA sequences handling (BLAST, Retrieving from databases, Alignment...)
 * Connection to Genbank, allow for the design of new parts from scratch
 * I suspect that this first point would be really great to expand upon. How will these classic sequence handling and analysis tools be used?  What might the work flow look like?
 * Automatic conversion of DNA sequence into a standard part: adding BioBricks™ suffix and prefix, removing Biobricks cloning sites from the sequence.
 * Codon optimization tool
 * Embed a DNA signature tool
 * Heuristics search
 * Check for weird secondary structures in any RNA that would be derived from said part; in particular, pay attention to possible oddball secondary structures that might arise across part-part junctions.
 * Connection to the Parts Registry
 * Handling of registry parts
 * Building new parts with existing ones
 * Easy submission of new parts
 * Datasheet attached to each part
 * In the long term, assembling of parts together
 * Support for different biobricks format
 * Graphical interface
 * Clever, help in design for non experts ( frameshift, stops, codon optimization, hairpins, etc...)
 * Ultimately, composition of parts and prediction of their behavior based on metadata attached with each part.
 * iGEM 2009 teams could serve as testers and debuggers?
 * How will this tool contribute in increasing the quality of the parts in the registry?
 * When a new part is designed or an exiating part is use, it came up with a datasheet attached. This datasheet contain standard specifications ( specified in Canton's paper). The user can fill the different specifications with experiment, the program can explain how to perform the experiment, make  regular update in the regitry. A datasheet including including all experiences is updated for each user.
 * How could we use such a tool to attract people outside from the field, contribute to the growth of the registry?
 * Basically, there's a lot of potential parts which are already characterized and stored in biology labs freezers.....If I just ask my friends to submit a part to the registry, they won't have time to do that, because they must understand all the requirements to build a part. But, if they just have to put the sequence into a programm which them do the job that would make things easier.  Then the program could be a tool which give them a benefit in their research even if they do not do Synthetic Biology ( Tool for biologists, need to work on that).


 * Randy Rettberg's Items to Consider
 * How will the application handle the wiki information, references, user comments, and images (not all parts have this, but they should)?
 * How will the application take in the current documentation of F2620 and do something good and then store it back?
 * What will the application do about the physical locations? Quality control?
 * How will the application deal with the access control and group membership?
 * We would like a new sequence and features editing system. One that could suggest features it finds. It could be written in Javascript.  Austin wrote a prototype in a Google Java to Javascript system. But it is not ready for further work.
 * The registry has a way to enter the "Hard information" about a part. That includes the subparts and scars for a composite part and the sequence and features for a basic part. I plan to modularize this interface so that users can use different implementations of the composite part and basic part designers.  Someone can make a much better graphical editor.
 * For each part, the Registry will have a "Tools" menu along with each part so that the existing CARGO tools are easier to use. It will be possible for others to add tools to the menu. The tools will be available for the user to select.


 * BioBrick Studio Mobile
 * Foyer
 * Show new published articles in synthetic biology. This search could be tailored to your specific needs e.g. by adding relevant keywords.
 * Show any changes (e.g. availability, new comments, etc.) in a set of parts you want to monitor.
 * Library
 * List the "Recent" BioBrick parts
 * List the BioBrick parts by category
 * Provide a means to study the details of the features in a BioBrick Part
 * Fetch the long description
 * Support keyword search
 * In the sequence viewer, increase the size of the label based on the size of the sequence
 * Present the DNA sequence as a graphical object that can be "flicked" left and right
 * Allow for the sequences to be viewed in the portrait and landscape orientations
 * Provide a means for easily emailing the developer of the part
 * Once you select a part offer suggestions for similar parts
 * Canvas
 * Allow for changes of the individual nucleic acids
 * Pinch/Spread through the levels of abstraction
 * Levels of Abstraction
 * BioBrick Part Features (eg. Promoter, RBS, etc...)
 * Secondary Structures
 * Primary Sequence

Discussion with Doug Densmore about Clotho
Douglas Densmore 18:50, 13 April 2009 (EDT)

Here is the list of BioBrick Studio features taken from below. The comments reflect Clotho's status on these tasks. Hopefully this will help to better explain the overlap. Currently (in my opinion), Clotho already does pretty much everything BioBrick studio wants to do. A simple collaboration model would be to write new Clotho plug-ins as opposed to writing a whole new tool. I am not sure a new tool is needed. Just my 2 cents (admittedly biased).


 * Classical DNA/RNA sequences handling (BLAST, Retrieving from databases, Alignment...)
 * Connection to Genbank, allow for the design of new parts from scratch
 * Clotho already does this. It reads Genbank (not the fully featured form yet; just a technicality) and can build new parts. It can also build new composite parts and then program liquid handling robots (e.g. BioMek 3000) to perform specific protocols (currently implementing one in Anderson lab for 2ab assembly) to physically assemble them in a quasi optimal way. Clotho has all the bells and whistles of ApE plus smarts about biobricks. The workflow environment we are working on can send sequences to BLAST and use the results.
 * Automatic conversion of DNA sequence into a standard part: adding BioBricks™ suffix and prefix, removing Biobricks cloning sites from the sequence.
 * Done in Clotho. In fact we have a plug-in devoted to this as well as a "parts packager" which exports data, packages it as a part based on database info, and then saves it back to the database.
 * Codon optimization tool
 * Gene Designer by DNA 2.0 has this. The algorithm is freely available. I could right a plug in to do this in 1 day. Probably going to do this in the summer if there is interest.
 * Embed a DNA signature tool
 * Unclear on what this is? If it is an algorithm, you just write an algorithm for the Clotho algorithm manager:)
 * Heuristics search
 * Check for weird secondary structures in any RNA that would be derived from said part; in particular, pay attention to possible oddball secondary structures that might arise across part-part junctions.
 * This sounds like a great plug in to write. We were going to import mFold so this might be a natural next step.
 * Connection to the Parts Registry
 * Handling of registry parts
 * Building new parts with existing ones
 * Easy submission of new parts
 * Going to import Davidson's viz-a-brick into Clotho this summer (talks to the registry). Handling registry queries are easy. The question is what do we do with the data? This could also be a Clotho workflow with Kepler (our summer project).
 * Datasheet attached to each part
 * A datasheet viewer is in the works for Clotho as a plug in. I have seen the nature biotech paper on datasheets. I would love to add this:)
 * In the long term, assembling of parts together
 * Already done in Clotho. Fast, close to optimal algorithms already written here.
 * Support for different biobricks format
 * This is a simple swap of a plug-in. We have the BioBrick "b" version of the plug-in already written.
 * Graphical interface
 * Clotho is a GUI. We are going to add at least three other views of DNA information at different abstraction levels this summer. Going to take at least the BioJADE code for its views and import them.
 * Clever, help in design for non experts ( frameshift, stops, codon optimization, hairpins, etc...)
 * Sounds good. Again no reason why this can't be in Clotho.
 * Ultimately, composition of parts and prediction of their behavior based on metadata attached with each part.
 * The holy grail:)
 * iGEM 2009 teams could serve as testers and debuggers?
 * Berkeley iGEM 2009 and Davidson (hopefully) will be helping with Clotho this summer

BioBrick Studio Mobile

 * Robert 12:33, 5 June 2009 (EDT):When you search for a part, you get X number of possible parts. When you scroll down and click NEXT on the bottom, it goes to the next page, but it still stays on the bottom of the page, it doesn't go to the top. It would be nice if it went to the top (I hope this is making sense).

General

 * Use a studio motif
 * Foyer - Entry point for the application
 * Library - Area to study natural or non-standard DNA sequences, basic and composite parts
 * Palette - Developers personal collection of DNA sequences, basic and composite parts
 * Canvas - Design environment DNA sequence refinement, basic and composite part development
 * Services - Area to explore the availability and cost of implementation services