mPartsRegistry is a simple interface to the Registry of Standard Biological Parts aimed at mobile smartphone browsers. It’s powered by the Parts Registry API, which provides a simple RESTful interface to key metadata about parts in the database. It features:

• . A simple interface tailored for mobile WebKit browsers (Android browser, mobile Safari, probably others). Web-based, zero-installation required.
• . Basic search of the Registry by part name.
• . “Favorite parts” to locally bookmark parts on your device.
• . Provides basic metadata associated with parts, including size, description, authors, DNA sequence, categories and availability.
• . Freely available and recyclable source code, released under the MIT License (fork it on GitHub).

The idea for a mobile interface to the Registry came out of a moment in the wet lab, where I was supervising the Monash iGEM team, and someone asked “How many basepairs is that part again ?”. I’ve found most ideas for smartphone apps in the lab a little contrived; nothing more than an excuse to jump on the Android or iOS app bandwagon, with limited practical utility. This was a situation where I could genuinely see a use for a simple mobile interface to look up some reference information, so I thought I’d create it.

The goal is not to completely replicate the functionality of the Registry (at this stage the API would not allow that anyhow), but to provide simple mobile-friendly interface to quickly look up important data about a Biobrick(tm) parts in a laboratory setting, where accessing a desktop computer is often less convenient. In this context, you generally know the part name (eg B0034) that is written on a tube, but would like to quickly lookup some details.

The project consists of two main parts: the web frontend, build using jQTouch and Django templates hosted on Google App Engine, and the parser backend (partsregistry.py) that deals with directly querying the Registry API.

The application uses BeautifulSoup on the server side to parse the XML served by the Registry’s API. This parser may be useful as a generic Python interface to the Registry API for other projects, although it is not yet feature complete. Why parse the XML on the server rather than the client ? The Registry API does not offer JSONP callbacks, making direct client-to-API queries by a web app served from another domain tricky (Same Origin Policy, yadda yadda). While this probably could have been done in straight clientside Javascript if I’d used some type of cross-domain AJAX hack, parsing on the server side also opens the possibility in the future to ‘value-add’ to the data in some way, potentially incorporating extra data not served directly by the Registry API, before it’s sent to the client.

Google App Engine works as a cheap hosting solution for a low traffic app like this, which is likely to stay within the free quotas. Also, GAE supports Python, and I like Python. jQTouch makes for a reasonable cross-platform mobile web interface, since it is optimized for WebKit-based browsers. While officially jQTouch supports iPhone/iPod Touch and doesn’t have official Android support, in my hands it works well enough on Android (and in fact displayed some minor bugs on Mobile Safari that were not evident on Android). Typically when using jQTouch you are expected to load multiple ‘pages’ all into several div-sections, lumped into a single HTML document. jQTouch then does the Javascript+CSS magic to render fast page switching, which actually working within a single HTML document. Since the main action of this app is to ‘search’, we don’t yet know what the results page will be, so this nice feature of jQTouch is barely used.

Searching for the same part all the time can get annoying, so mPartsRegistry provides a simple ‘bookmarking’ feature where a list of favorite parts can be managed and stored on the device. This is implemented via HTML5 localStorage – if there was demand then this could easily be turned into server side storage, but I doubt it’s necessary. In the future, it might make sense to pre-cache the metadata for any of these “favorite parts” so that the fast page switching features in jQTouch can be used to full advantage.

Currently, the interface does not show information about sequence features, subparts and twins, however I plan to implement these at some point. The Registry API currently does not provide information about samples, literature references or lab groups, but once these are enabled I plan to support this metadata within mPartsRegistry too.

Okay, that’s all kids .. and remember .. take off your gloves before using your smartphone in the lab !

Around three weeks ago I attended the Synthetic Biology 4.0 meeting in Hong Kong, hosted by the Hong Kong University of Science and Technology. I’ve taken a little time to allow all the new and exciting ideas to sink in. I really enjoyed the meeting, and while it was a little short it was an effective way to quickly sample the current developments in synthetic biology, as it stands.

Some highlights

Here are some summaries on a few highlight presentations. Due to parallel sessions, I couldn’t see every talk; luckily I’ll be able to catch up on those I missed once the videos appear online.

Clyde Hutchison (J. Craig Venter Institute), spoke about genome construction, specifically about rebuilding the minimal genome on Mycoplasma genitalium by synthesis of large fragments and subsequent stepwise assembly. This is probably not brand new work, but it was the first time I’d seen it presented. Turns out they could fully assemble the genome into a yeast vector from 25 large fragments using a ‘shot-gun’ approach with subsequent PCR screening to identify the correctly assembled construct.

Christopher Voight (UCSF) (and a poster presentation by Travis Bayer et al): Bio-MeX: A Novel Route from Biomass to Gasoline and Petrochemicals. Chris spoke about the work his lab is doing on producing methyl halides in E. coli and yeast. Methyl halides are a common feedstock in the petrochemical industry for producing many other organic chemicals, so a non-fossil fuel source will be useful in the future. I’ve always been a little skeptical about ocean metagenomic studies that sell themselves as the solution to the worlds energy problems, based on the notion that an amazing new enzyme will be discovered in marine bacteria. Well, this work coming out of Chris’ lab could prove me wrong … after screening 89 putative homologs of a methyl halide transferases from the various kingdoms of life (most annotated ‘methyl transferase’ in sequence database), the best one turned out the be from an “uncultured marine bacteria”, discovered by the Sargasso Sea Sequencing Project.

Eric Winfree (CalTech) spoke about his experiments with DNA tile-based crystals, as a potential model system for pre-biotic life. Crystal growth, breakage and regrowth models replication, the tiled ‘layers’ of different crystal variants form the genome. Don’t be mislead and assume that Eric is proposing that DNA of this nature was actually around in the primordial soup … it’s simply being used as a well understood system enabling specific molecular complementarity and template based replication (with errors); in theory this type of system could be built using any ‘crystal’ with similar properties.

Jay Keasling (UC Berkley, LBNL): Fuel and Drug Production: Jay gave some facts and figures about biofuel production from the metabolically engineered organisms which are ultimately being commercialised at Amyris. It was noted in the opening slides of several talks at this conference: Ethanol is not considered a very good gasoline replacement (lower energy density, too hydroscopic for existing pipeline infrastructure, high octane rating) when compared with n-butanol (higher energy density, less hydroscopic, controlled volitility, similar octane rating to gasoline). Watch the video for some well handled but potentially hairy questions about the source of feedstocks for biofuels production. On the science-side, Jay showed some interesting results from studies testing the effect of scaffolds for co-localising enzymes in a biosynthetic pathway of interest (as fusion proteins to PDZ, SH3 etc domains). After screening a library of scaffolds that would arrange different numbers of enzymes in different orders, one specific arrangment (“A-B-B-C-C”) worked better than other variations. No rational explaination, but interesting nonetheless.

Patrick Boyle et al from Pamela Silvers lab:  (poster presentation, The Synthetic Hydrogenosome: Subcellular Engineering for Biohydrogen production): showed how he was engineering yeast mitochondria for hydrogen production by introducing components of the pathway responsible from hydrogenosomes. This work caught my interest since for the past few years I’ve worked on aspects of protein import into mitochondria and related organelles (including a little bit of collaborative work on hydrogenosomes recently). Early versions of the engineered strain were producing small amounts of hydrogen compared with wildtype yeast … it will be interesting to see how far this can be optimized in the future (I don’t expect it to fuel a hydrogen economy anytime soon, but it’s early days).

Priscilla Purnick (Yale) spoke about her work helping engineer embryonic stem cells with genetic circuits to precisely control proliferation, differentiation and cell death, with the ultimate goal of treating Type I Diabetes with self-regulating beta-like insulin secreting cells. I couldn’t do justice to the technical details in a short summary here, needless to say it’s complex and impressive looking work. This was a spin off project from the Princeton iGEM team using many ‘off the shelf’ BioBricks(tm). While still in the early stages, the talk showed a nice mix of systems biology style modeling and hard experimental data.

I sat in on an open discussion session, entitled Legal Schemes and Rights. The key point that surprised me here was how little had actually been figured out surrounding the ‘intellectual property’ law of sharing, modifying, combining and (potentially) commercializing individual BioBrick[tm]-style parts, and devices built with such parts. I’d been under the delusion that the legal side was figured out early on, and that BioBrick parts were shared under some sort of MIT-like or BSD-like license. This is apparently not the case. Various possible legal frameworks were outlined, but I think the most insightful advice I heard was something to the effect of (paraphrased) .. “Don’t sit around treating this like an interesting academic problem .. pretty soon (~12 months ?) community norms for licensing parts will emerge by necessity and under the force of commercial interests, not by careful or considered design, and if you haven’t worked to establish things in the way that is best for proliferation of the technology and all stakeholders, it will be too late to change course. We have seen this has happen in other industries, it will happen here too”. Watch the videos once they appear if you want the correct quote, I can’t remember who said it now

I’ve half written a “part 2″ to this post, outlining some ideas on the current state of Synthetic Biology as a field … but I’ll probably never publish it since it’s mostly just me organizing my slightly opinionated thoughts out loud. The summary is: there is currently a lot of excitement, potentially a little hype (see Gartner’s hype cycle, pick where you think Synthetic Biology currently sits on the curve). It will be interesting how this pans out, particularly if expectations have been unrealistically inflated. There has also been a bit of quibbling over the definition of Synthetic Biology; those engineers that have forged the field are probably pretty bored of the old ‘definition debate’ by now, but many biologists still don’t really know what Synthetic Biology is. Based on discussions I’ve had with colleagues about the conference content upon returning, the average molecular biologist doesn’t always see how Synthetic Biology is very different to what various bioscientists have been doing under the banner of Biotechnology for many years. My simplest explaination is that the underlying technologies are essentially the same, but the approach, the application of formal engineering principles and their use in a rational way to create useful ‘devices’, is different from past practices that have largely focused on discovering new knowledge about biological systems with many useful technologies arising in a more ‘undirected’ and opportunistic fashion. It’s great to be living in a time when the foundational knowledge in biology, built on decades (centuries?) of basic research, are slowly beginning to come to fruition in rationally designed technologies.

For another perspective, and little more on the buzz outside of the formal presentations, see Jonathan Clines “Word on the Street @ SB 4.0″ posts.

Some opinion, analysis

This is a blog, so a post like this wouldn’t be complete without some opinionated analysis . My daily work involves molecular biology, structural biology encompassing some basic protein engineering, and some bioinformatics. I don’t currently practise anything I would consider bona fide synthetic biology, although I’m comfortable with the technology, concepts and language used. Synthetic Biology is a relatively new field (or as some would argue, a relatively new term for the intersection of some established fields), and as a result things are developing rapidly, both on the technology side, and on the ethical/social/legal side. The push to acquire mindshare and funding for exciting but speculative biotechnologies has generated some big claims, and some big expectations.

Gartner’s hype cycle (modified version used under a CC Share-alike license, 3.0, original image by Jeremy Kemp).

My overall feeling is that we are just passing the peak of inflated expectations. Although to be fair, it’s a little tough to pick a single point on the hype curve for “Synthetic Biology” at this point. It seems like there are lots of “micro-hype curves” already playing out, as different groups use the the new tools that have become accessible to engineer something cool and useful and test their design. Sometimes things work reasonably well, other times it becomes clear that the biological systems that have evolved under natural environmental pressure are not always modular and easily abstracted. That is not to say the once those systems are adopted, tweaked and tested by engineers (potentially via directed evolution), that they will not become predictable, modular and abstractable components; this is the assumption that the success of synthetic biology as an engineering disipline is relying on. Tweaking and characterization of basic components is still a work in progress. The outcome of the ongoing standardization of parts and subsequent predictability of completed devices should reveal just how soon and how deep the impending “Trough of Dissillusionment” will be.

(it should be noted that the common cry from biologist that ‘biology is not aways predictable’ and ‘what about emergent behaviour’ can be simply avoided by not using the parts that don’t behave. This could be a severe limitation, where parts with certain functions are scarce or unavailable due to their unpredictable nature. The same biologists dismissive of the claim that biological components can be abstracted and standardized will turn around and defend their use of GFP / FLAG and HA-tags as a standard method for detecting the location of proteins in cells. Unpredictable behaviour in these systems often occurs, but is often downplayed).

Overheard at the banquet: “I wish people would just stop trying to define it”.

As with any new field in the process of carving out an identity, there have been various attempts to define “Synthetic Biology”, and as expected not everyone agrees. In fact, I get the sense that people working on bona fide synthetic biology projects seem to have become a little sensitive about it, to the point that I half expect to be ‘flamed’ for speculating about the technology hype curve above, and chastised for dredging up the definition debate again (which has probably become pretty stale and repetitious for some).

I think the definition from the NEST High Level Expert Group is reasonable:

‘Synthetic biology is the engineering of biology: the synthesis of complex, biologically based (or inspired) systems, which display functions that do not exist in nature. This engineering perspective may be applied at all levels of the hierarchy of biological structures—from individual molecules to whole cells, tissues and organisms. In essence, synthetic biology will enable the design of ‘biological systems’ in a rational and systematic way’

The key term here is engineering … not as in ‘genetic engineering’ which historically has been more haphazard due to the limitations of the tools available, but engineering based on strict engineering principles. Compared with most other scientists who are using effectively the same technologies and protocols in molecular biology, the ‘synthetic biology engineer’ aims not only to understand the system that they are studying, but pragmatically take well understood biological components and systems and put them to good use.

From large parts of the scientific program from the SB 4.0 conference, you could be lead to believe it was all about metabolic engineering. Or maybe whole genome synthesis, or genetic circuits. The SB 4.0 website defines it as:

Synthetic Biology is a new approach to engineering biology, with an emphasis on technologies to write DNA. Recent advances make the de novo chemical synthesis of long DNA polymers routine and precise. Foundational work, including the standardization of DNA-encoded parts and devices, enables them to be combined to create programs to control cells.

It goes on to list examples of some real-world applications for synthetic biology: BioEnergy, Drug Production, Materials and Medicine (aka programmed cells as therapeutics). All of these examples, other than “Medicine”, ultimately relate to metabolc engineering … heavily tweaking (or entirely rebuilding) a biosynthetic pathway in a host cell, usually E. coli or yeast, to produce something we currently dig up from the ground and transform into fuel, chemicals or materials through the petrochemical industry.

Another angle is Luis Serrano’s distinction between Biotechnology vs. Synthetic Biology:

Thus, improving the production of a certain metabolite by tinkering with some of the components of a metabolic network will fall within the realm of Biotechnology. On the other hand, the introduction of several exogenous enzymes in an organism to produce a new compound will fall within the scope of Synthetic Biology.

I find it hard to agree with this particular division. The introduction of heterologus genes, and the production of a ‘new compound’ seems like a logical extension of advanced metabolic engineering, as a subfield of ‘biotechnology’, and barely warrant reclassification into an entirely new field. Unless you need a name change for marketing purposes …

There is a proven model for attracting interest (and hence funding) to a field by changing the name in response to new possibilities through some enabling technology; think gene sequencing vs. genomics, protein identification vs. proteomics, studying metabolism and cell signalling pathways vs. systems biology. In this case, cheap high-throughput sequencing and relatively cheap DNA synthesis are allowing engineers to do things they couldn’t before. So the biotechnology and genetic engineering of the past becomes … synthetic biology.

Names and definitions aside, (synbio)technology has got the the point where we are able to do some pretty cool things using biological systems … and if a little re-definition helps people acknowledge that, then all the better.