Posts by Jonathan Cline

A great article in the recent PLoS Computational Biology – freely accessible to all!  Additionally, check out: OpenWetWare’s topic on “R”.

A Quick Guide to Teaching R Programming to Computational Biology Students

by Stephen J. Eglen^*, Cambridge Computational Biology Institute, Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000482

The name “R” refers to the computational environment initially created by Robert Gentleman and 1 Robert Ihaka, similar in nature to the “S” statistical environment developed at Bell Laboratories (http://www.r-project.org/about.html) [1]. It has since been developed and maintained by a strong team of core developers (R-core), who are renowned researchers in computational disciplines. R has gained wide acceptance as a reliable and powerful modern computational environment for statistical computing and visualisation, and is now used in many areas of scientific computation. R is free software, released under the GNU General Public License; this means anyone can see all its source code, and there are no restrictive, costly licensing arrangements. One of the main reasons that computational biologists use R is the Bioconductor project (http://www.bioconductor.org), which is a set of packages for R to analyse genomic data. These packages have, in many cases, been provided by researchers to complement descriptions of algorithms in journal articles. Many computational biologists regard R and Bioconductor as fundamental tools for their research. R is a modern, functional programming language that allows for rapid development of ideas, together with object-oriented features for rigorous software development. The rich set of inbuilt functions makes it ideal for high-volume analysis or statistical simulations, and the packaging system means that code provided by others can easily be shared. Finally, it generates high-quality graphical output so that all stages of a study, from modelling/analysis to publication, can be undertaken within R. For detailed discussion of the merits of R in computational biology, see [2].

The following is a cross-post from the 88 Proof Synth Bio Blog.

“BIO hosted a round-table discussion with leading-edge companies on technical and commercial advances in applications of synthetic biology. Speakers in the session represent leading firms in the field, Amyris, BioBricks Foundation, Verdezyne and Codexis.”

This industry-centric conference call prominently mentioned “hobbyists doing Synthetic Biology in their garages.” The Progress in Commercial Development of Synthetic Biology Applications podcast can be listened to at this link.

BIO is a biotechnology advocacy, business development and communications service organization for research and development companies in the health care, agricultural, industrial and environmental industries, including state and regional biotech associations.

Below are my notes and summary from the conference call. (Disclaimer: all quotes should be taken as terse paraphrases and see the official transcript, if any, for direct quotes.)

BIO:

“BIO sees synthetic biology as natural progression of what we’ve been doing all along [previous biology and biotech commercial research]. […] Industrial biotechnology gives us tools to selectively add genes to microbes, to allow us to engineer those microbes for the purposes of [biofuels] or production of other useful products. Synthetic biology is another tool which allows us to do this, and is an evolutionary technology, not a revolutionary technology. It grows out of what our companies have always been doing with metabolic shuffling or gene shuffling, etc. [Synthetic biology] has become so efficient that new ways of thinking about this field are necessary. We are beginning to build custom genomes from the ground up, a logical extension of the technologies [biotech companies] have developed. […] “

Industrial biotechnology’s phases:

1. Agriculture (previous phase)
2. Heathcare (previous phase)
3. and today’s phase: biofuel production, food [enrichment], environmental cleanup

Challenges in today’s world are: energy and environment (greenhouse gases, manufacturing processes, … how to also develop these in the developing world); Synthetic biology can help to address these problems.

“Every year the development times [of modifying organisms for specific tasks] are shortened [due to availability of more genomic information].”

“There is unpredictability in synthetic biology [however] this is still very manageable.”

This comment was a response to a ‘fluffy’ question about the ‘risks/dangers’ of the technology.

“[This technology is accessible because as we have heard in the news] there are now home hobbyists experimenting with this in their garage laboratories.”

Hmm; I wonder who they are talking about..

Amyris:

“We have been moving genes around for quite a while. [The difference today which yields Synthetic Biology is that] we can do things easily, rapidly and at small [measurement] scale.” Synthetic biology allows scientists to integrate all the useful [genomic, bioinformatics] data into a usable product [much more rapidly than before]. Previously it would take months to modify a microorganism, now we are down to 2-3 weeks [which is] limited only by the time required for yeast to grow [and we aren’t looking to speed that part up]; this is a rapid increase in the ability to test ideas and [measure] outputs. We view synthetic biology as very predictable [in the sense that un-intended consequences are inherently reduced]. We engineer microorganisms to grow in a [synthetic environment for fermination in a ] steel tank which reduces it’s ability to grow in a natural environment [thus] the organism loses out against environmental yeast [so modified organisms won’t cause problems in the environment since they will die]. We need more people who can understand complete pathways, complete metabolisms.”

Verdezyne:

“Synthetic Biology is a toolset to create renewable fuels and chemicals. […] The benefits of Synthetic biology are, 1. profitability, as sugar is a lower cost of carbon; 2. efficiency, from use of [standard high efficiency] fermentation processes; 3. from efficiency improvements, this improves margin, 4. decreased capital costs; 5. Use of bio-economy, using local crops [for biomass] or local photosynthetic energy to yield [chemicals for local use]. Now we can explore entire pathways in microorganisms [compared to previously when we could only look at single genes]. Traditionally, chemical engineering is the addition of chemicals to create a functionality [whereas in microbial engineering the microorganism directly creates the outputs desired]. We retooled for synthetic biology very easily [from originally building chemical engineering systems].”

Codexis:

“Biocatalysts [are] enzymes or microbes with novel properties [for commercial use]. Green alternatives to classic manufacturing routes. Biocatalysts require fewer steps and fewer harmful chemicals. Synthetic biology is one tool towards this [to] quickly create genes and pathways [using the massive amounts of genomic information now available]. [Use of] Public [genome] databases [allow us to] chop months off the [R&D] timeline. [One desire] of scientists in synthetic biology is making the microorganisms [predictable, as in in engineering] however in commercial environments we can make variants very quickly [so we can deal with variants]. There are many companies which focus on commodification of biological synthesis and we use a variety of suppliers. The analysis [the R&D] required for designing new pathways is [what is lacking in skillsets of today’s biologists].”

Drew Endy:

Patents costs are drastically more than the cost of the technology itself. The technology of the iGEM competition costs $3-4 million per year for all international teams, whereas the costs of patenting all submitted Biobricks every year would be 25k per part for 1,500 parts for a total of over $37 million dollars; thus, the patent costs are much more expensive than the technology, so this is an area which is being worked on. The next generation of biotech is hoped to “run” on an open “operating system” made from an open foundation [where new researchers can use existing genetic parts as open technology rather than having to build everything from scratch].

(For my further editorial, go to the full post at 88 Proof Synth Bio Blog.)

There you have it. Synthetic biology is the leaner, meaner biotech for the future.