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BioCompiler might start life as BioCOBOL

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Update: Matthew has found an even more thorough review paper that discusses computer assisted synthetic biology approaches — it can be found at doi:10.1016/j.copbio.2009.08.007.

The iGEM competition year is running to a close. The teams are headed into November 2010 and have roughly one month left before attending the conference. I’m personally not attending the conference this year — I think the undergraduates will get more out of the experience.

The current year sees our continued efforts to precipitate a dedicated software team — a functioning autonomous unit that will serve to supplement and enhance Waterloo’s impact in the iGEM competition. More importantly, we’re going to do some very interesting science. We’ve had some success talking with other student groups across campus — notably, we should probably talk with the student IEEE/CUBE chapter when we have more work completed. We had involved BIC as well, however, it was early on and we had even less ground to stand upon ( — the primordial software team was mostly interested in BioMortar and BrickLayer at the time — the later project having been taken up by the iGEM Coop students as in Python this year).

This whole BioCompiler business started when Matthew uncovered a nice candidate problem: the compilation of a schematic for behaviour to a fully functioning synthetic biological circuit. Let’s be as precise as we can be here. I mean to say, we will take a description (which could resemble a piece of formal language source code) — and have it compiled into the sequence of BioBricks that will produce the desired behaviour.

This idea has been approached by several groups before — but each time, a different subproblem was considered (this is a reorganization of Matthew’s very nice list here).

  • Synthetic biology programming language: Genetic Engineering of Living Cells (GEC) (Microsoft Research) is a project that hones in on a formal language specification.
  • Synthetic biology computer assisted design (CAD): Berkeley Software (iGEM 2009) created a suite of items — Eugene (formal language for synthetic biology), Spectacles (visualizer integrating parts with their behaviours), Kepler (a dataflow broker). As well, Berkeley is responsible for the award winning Clotho (iGEM 2008 – Best Software Tool) which is a workbench that connects with the parts registry database (amongst other possible resources).
  • Systems biology pathway reaction simulation: Systems Biology Markup Language (SBML), Systems Biology Workbench (SBW) and Jarnac are a set of tools that perform systems biology analysis (which we consider to be an output of synthetic biology). SBML is the formal language, Jarnac is a reaction network simulator (which utilizes JDesigner as a front end) and SBML is a dataflow broker between SBML and Jarnac.
  • BioBrick specific pathway simulation: Minnesota’s Team Comparator (iGEM 2008) created SynBioSS — a tool which estimates the concentration of reactants and products given the appropriate BioBricks on a simulated circuit.

Update — here are a few more items thanks to Matthew Gingerich, George Zarubin and Andre Masella.

  • Molecular biology and bioinformatics analysis: The European Molecular Biology Open Software Suite (EMBOSS) is a toolkit developed by the European Molecular Biology Network (EMBnet) for bioinformatics. This might not be immediately relevant, but it is interesting. EMBOSS is actually relatively complete. More distantly along this vein, there’s also Bioconductor which focuses mostly on microarray analysis and is implemented in R.
  • More synthetic biology computer aided design (CAD): TinkerCell is a GUI-driven piece of software that supports extension with C++ and Python. TinkerCell along with the suite created by Berkeley Software are the two most promising target systems in which to integrate BioCompiler. Finally, there’s GenoCAD which appears to be in an early phase of development — this software looks to emphasize construction with correct syntax and attribute grammars — I’ll have to read more about this.
  • Formal laboratory protocol description: BioCoder is another Microsoft research project — the designed language aims to be both human readable and complete for automation. It reminds me of standard operating procedures (SOP) with greater precision. While BioCoder compiles from protocol to automation, we’ll be compiling to circuitry and protocol. BioCoder will give us some insights about the kinds of protocols that others are thinking of.

There is of course more software, but these are the items that we have become most familiar with — that we like — and that we consider to be standards toward which our own work should strive.

Two interesting problems arise when we think about these subproblems. First, the programming languages specified (including Eugene from Berkeley’s CAD suite) are exactly what they claim to be. Formal specifications. This is possible because of how concrete they are. They literally document what a synthetic biology circuit is. But this isn’t too different from what humans have been doing in iGEM all along. Second, the synthetic biology items don’t really seem to talk to the systems biology items — whereas we expect that the two — being input and output — to be inextricably linked. I explain my thoughts on the two below.

Why a programming language?

Andre enlightened me to this the other day. Humans invented programming languages to do two things. On an arrow running from the concrete toward the esoteric, we have the practical concern of compressing the amount of code that we want to write while retaining our programs’ expressiveness. This is the origin of macro systems such as COBOL. On an arrow pointing in the reverse — from the cerebral abstract down to the literal — we have the theoretical concern of mathematical beauty, of completeness. This is the origin of such functional languages like Lisp. For humans to have any hope of creating such a Lisp-like language for synthetic biology — we would need to understand all of the reactionary nuances about it, the system with which we tamper — at least inasmuch as a painful heuristic approximation. This is a feat we are no where near completing though footholds are managed with systems biology.

So here we are, BioCOBOL is the first step. A developing simple — though complete macro-like system that is in league in terms of abstraction with the programming language / CAD -like projects we’ve seen thus far. Only, we aim to increase the efficiency of circuit design; so that the programming language is not a literal mapping of the human document — rather, it is an explanation of behaviour. We will abstract it ever so slightly with each iteration of development — departing further and further away from CAD. A subteam headed by Brandon is currently developing the syntax and search algorithms required for the job — Brandon suggests that a weighted traversal of valid circuits should form our algorithmic primitive. My subteam is attempting to characterize as many known circuits in iGEM as possible — analyzing what pieces of input (stimuli: chemical concentrations, gradients, quora, oscillators) may be compressed for their common usage — what function prototypes already exist ( — reacts to an input: promoters) for compression — what the standard outputs are (analogy to printing error messages: GFP-family) etc. — again in the effort to realize what is losslessly compressible. Our software should eventually provide the correct laboratory protocol as well.

In this sense, we are respecting what a compiler is before we even approach more sophisticated compilation: it transforms a document in one language to another.

Incidentally, I should mention that Jordan and George are working on a modelling problem with the lab team — I’m not clear on the specifics, but I take it they want to pull out some differential equations on a set of promoters.

Why do we care that Synthetic Biology logic should talk to Systems Biology logic?

Finally, it is clear that we will eventually want to become even more abstract — even more mathematically complete, even more expressive. While we may never know enough about systems biology to create BioLISP (in our lifetime), we expect there to be sufficient research for us to discover — and perhaps research we can conduct ourselves to come ever closer. Systems biology allows us to think about synthetic biology in terms of reaction concentrations; free energy etc.. It gives the notion of compilation its own ground; the ground we want to cover. Imagine the perfect BioCompiler — stating the a problem to be compiled in terms of the input and output of the system. Let’s be precise here: I mean to say, the products and reactants or behaviour of our circuit. Let us describe what our circuit will do instead of what our circuit is made of. This — the missing link, this compiler — is the logical final step of BioCompiler.

Eddie Ma

October 26th, 2010 at 10:57 am

The Return of Phi C31

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I’ve been so out of the loop with iGEM over the last month. I’ll need to figure out how to get back into the swing of things, probably starting with the post mortem meeting on Tuesday. Generally, since no new maths could be put on the table that actually encompassed the problem well– the brute force approach was kicked into high gear with a few more filters to increase the probability of success.

Call these “System Filters” since they aren’t really based on biologically significant concepts, really just sanity checks that are conceptually consistent with the project (i.e. we’d run out of hard disk space otherwise…). Significantly, Matthew implemented “Blank Stare”, which destroys reactants that exceed a given length (thus preventing them from hogging the CPU looking for less parsimonious solutions). Less significant were Andre’s “Lone Gunman” which deletes arbitrary chromosomes with stochastic efficiency and my “Tag” which prevents chromosomes from cross reacting.

(On second thought, “Tag” IS a “Biological Filter” not a “System Filter” because it removes redundancy by implementing the rule that we only admit bacteria that have exactly one chromosome.)

I should mention that “significance” above isn’t about the triviality of the code, it’s about the amount of anticipated efficiency boon we’d gain from an item’s deployment.

Tomorrow’s post mortem will continue the work I’ve started on our iGEM 2009 Wiki Modelling page… We’ll decide what we want to mention, how close we got to our solution and figure out how to precisely characterize the problem space uncovered by our various attempts.

Additionally, we should probably discuss the relevance of John’s attN site cloning and tests to see if the operators show any sign of degeneracy, and which ones in particular.

Finally, I should mention that Brandon has been working on a C++ port of the whole application we wrote in Python to elucidate how much the virtual machine impacted the performance of our solver– the team is quite divided on this idea with a big half (myself included) thinking that the exponential growth due to the algorithm is the greater factor– Brandon may have some answers for us when it’s up and running.