open source science

Robot Scientist Creates and Evaluates Microbiology Hypotheses

Jean-Claude Bradley — Sun, 04 May 2008 12:09:59 -0700

Description

From Ross King's Robot Scientist web site (1):

The Robot Scientist is perhaps the first physical implementation of the task of Scientific Discovery in a microbiology laboratory. It represents the merging of increasingly automated and remotely controllable laboratory equipment and knowledge discovery techniques from Artificial Intelligence.

Automation of laboratory equipment (the "Robot" of Robot Scientist) has revolutionised laboratory practice by removing the "drudgery" of constructing many wet lab experiments by hand, allowing an increase in both the scope and scale of potential experiments. Most lab robots only require a simple description of the various chemical/ biological entities to be used in the experiments, along with their required volumes and where these entities are stored. Automation has also given rise to significantly increased productivity and a concomitant increase in the production of results and data requiring interpretation, giving rise to an "interpretation bottleneck" where the process of understanding the results is lagging behind the production of results.

The research fields of Computational Scientific Discovery and Bioinformatics have emerged in part as a response to this bottleneck. Both disciplines use computational approaches from Statistics and Machine Learning to provide an "automated understanding" of the experimental results.

This is a strong signal foreshadowing the near automation of the entire scientific process. This robot is able to function within the framework of molecular biology. However, each field has its own set of opportunities and challenges. The difficulty in extending this concept to other fields, such as organic (2) or inorganic chemistry will depend upon the conceptual models used. Providing the system with fewer human-based rules about how chemistry works would make it more difficult but ultimately could be more interesting.

Coupled with the practice of Open Data (3) and Crowdsourcing (4), a new form of distributed scientific intelligence could emerge that would "understand" reality in the sense that it is predictive and able to control phenomena but not in a way that is necessarily intuitive to humans.

This may be a pathway to the technological singularity.(5)

Future of chemistry

Source

1) http://www.aber.ac.uk/compsci/Research/bio/robotsci/intro/
2) http://sciencex2.org/en/node/16263
3) http://sciencex2.org/en/node/15726
4) http://precedings.nature.com/documents/1505/version/1
5) http://en.wikipedia.org/wiki/Technological_singularity

Automation of Crystallization by an Academic Group

Jean-Claude Bradley — Sun, 04 May 2008 08:57:54 -0700

Description

Alastair Florence and colleagues report on the use of an automatic reactor platform from ChemSpeed (1) to accelerate the crystallization of organic molecules (2):

The principal gain over manual crystallization stems from the fact that automation enhances productivity, allowing the search for physical forms to be conducted systematically and reproducibly over a finer grid (e.g. larger solvent library) than might be accessible manually, increasing the probability of observing new forms. In practise, making due time allowance for set-up, sample retrieval and cleaning between experiments, experience has shown that 32 crystallizations per working day is sustainable. Further opportunity for productivity enhancement comes from integration of the platform control PC with an electronic laboratory information management system (LIMS) to provide effective archival, search and retrieval facilities for the recorded control parameters associated with large numbers of crystallizations.

Although High Throughput Synthesis (HTS) has become an integral part of the drug discovery process in companies, larger libraries generally come at a cost to purity and full product characterization.(3) There is still much room available to adopt more automation to the practice of organic chemistry, especially in academic labs. Koppitz and Eis predict (3):

Aside from the technology, we are now entering an era in which chemists working in AMC (Automated Medicinal Chemistry) will probably become more chemistry-oriented than they have been in the past decade, when the focus was on developing and implementing a robust and reliable technology platform. In this context, more chemistry related challenges, such as the discovery and exploitation of new structural motifs in chemical space, development of new chemistries and their application in library synthesis, will hopefully be addressed and solved.

This signal points to more involvement by academia into automating chemistry processes typically done manually. This is significant because there is a greater probability that results will be shared with the scientific community, compared to similar work done in industry.

Eventually it is possible that automation will enable even the open execution of chemistry experiments by leveraging crowdsourcing. (4)

Future of chemistry

Source

1) http://www.chemspeed.com
2) http://www.chemspeed.com/files/publications/sa/pa/2006_crystallization_o...
3) http://www.chemspeed.com/files/publications/sa/pa/2006_Automated%20medic...
4) http://precedings.nature.com/documents/1505/version/1

Open Source Drug Discovery

Jean-Claude Bradley — Fri, 02 May 2008 13:31:59 -0700

Description

Seema Singh writes in a recent Cell article (1):

Open source software may have been around for 17 years, but using an open source model to speed up drug discovery is a relatively new idea. This month, India is launching a new open source initiative for developing drugs to treat diseases such as tuberculosis, malaria, and HIV.

Bernard Munos reports on a similar trend in a Nature review (2):

The low number of novel therapeutics approved by the US FDA in recent years continues to cause great concern about productivity and declining innovation. Can open-source drug research and development, using principles pioneered by the highly successful open-source software movement, help revive the industry?

Stephen Maurer (3) writes:

Despite their novelty and importance, open source methods have been largely been limited to software. However, scholars have long suggested that it would be logical to organize at least one other field - drug discovery - using open source principles. This paper reviews today's relatively tentative attempts to organize open source biology collaborations and argues that more ambitious projects are feasible. Five specific projects are proposed and analyzed in detail. The article concludes by examining the special legal problems of writing open source licenses in the patent-dominated field of biology.

The theme of Open Source Science used for the development of drugs is one that arises often lately. The value for neglected diseases could be immense.

In these reviews, most examples fall short of being truly open in the sense that one normally thinks of Open Source Software. If data are made public, it is generally after an embargo period. Or data are shared, but only within a group of collaborators, who may have to pay to join the consortium.

The signal here is the strong interest in the concept of Open Science as applied to drug development. I don't think that this will abate and look for bottom-up data sharing initiatives to realize some of the objectives of the movement.

Future of chemistry

Source

1) http://www.cell.com/content/article/abstract?uid=PIIS0092867408004510
2) http://www.nature.com/nrd/journal/v5/n9/abs/nrd2131.html
3) http://papers.ssrn.com/sol3/papers.cfm?abstract_id=1114371

Uploading of Spectra on ChemSpider

Jean-Claude Bradley — Fri, 02 May 2008 10:30:15 -0700

Description

Antony Williams writes (1):

I’ve posted previously about analytical data deposition on ChemSpider. There are now fairly regular depositions going on and an increasing number of spectra are available online...We have now enabled the deposition of CIF files onto the system...We have also supported the submission of images to associate with structures.

ChemSpider (2, 3) is a free and hosted database service that allows users to search and contribute information about organic molecules. The recently introduced ability to upload spectra of any kind, including NMR, MS, UV, IR and X-Ray crystallography now permits individual researchers to store full characterization information proving the structure of their compounds.

In contrast to simply listing peak information, uploading the raw data (in JCAMP-DX (4) format for the most part) allows other researchers to zoom into any part of the spectra to confirm structure assignment and purity. Errors are far less likely to occur and propagate this way.

Although these capabilities have been available for some time on commercial systems for private use, the free public availability offered by ChemSpider is a strong signal that Open Source Science in chemistry will only become easier and more reliable over time.

Future of chemistry

Source

1) http://www.chemspider.com/blog/ability-to-add-images-and-cifs-to-chemspider.html
2) http://www.chemspider.com
3) Disclosure: I am on the advisory board of ChemSpider
4) http://sourceforge.net/projects/jcamp-dx/

Spontaneous Publication of Raw Research Data

Jean-Claude Bradley — Thu, 01 May 2008 15:46:18 -0700

Description

Despite the lack of extrinsic motivating factors, such as formal publication recognition or financial gain, some researchers have been attempting to post the raw data of their experiments using any means available, and often involving considerable work and care. (1)

Virtually every researcher has been doing this in a different way, reflecting not only differences between fields but also how the information is represented within each individual's mental framework. (2)

This is a clear signal that information wants to be free, or at least that is how it is behaving.

Going forward I would expect an increase in data sharing, irrespective of any change in the scientific research reward structure. I do not expect a single standard representational system to emerge quickly. It seems more likely that the data will be posted first, then later duplicated and converted to adhere to the conventions of various databases as they arise.

Redundant data has survival value.

As a recent example, Frank Gibson writes (3):

Several months ago - about 3, I made a public commitment to make the data I have generated during my Phd open and available online. Well I have not ignored this and in the interim I have been investigating various ways I can do this. Not only do I want to make it available but I want to structure it in a standard form, namely the gelML format. In addition, I was involved in developing it the specification and therefore, I have somewhat an obligation to use it. As it is an XML transfer format I needed to be make changes and revision it, like developing code, so in that sense recording the data on a wiki or blog would not be appropriate. For this reason I have chosen to create a google code project for gel electrophoresis data and do everything in subversion. You can browse the subversion repository or check it out anonymously. The geML file that will eventually (as its still very much a work in progress) contain the data is here. As I am doing this, I though I might as well publish my lab book while I was at it. This will be done using LateX and the pdf that gets generated can be found here.

Future of chemistry

Source

1) http://www.michaelbarton.me.uk/2008/04/relection-on-ons/
2) http://blog.openwetware.org/scienceintheopen/2008/04/29/protocols-for-open-science/
3) http://peanutbutter.wordpress.com/2008/04/30/open-ed-gel-electrophoresis-data/

Communicating Science with Blogs

Jean-Claude Bradley — Thu, 01 May 2008 10:39:33 -0700

Description

As reported in Nautilus (1):

The official forum for Science Blogging 2008, to be held at the Royal Institution, London, on 30 August 2008, has been set up at Nature Network.
The science blogging community is growing rapidly and reaching larger audiences. At Science Blogging 2008, science bloggers from around the world will have the opportunity to meet and discuss the pressing issues in science, science communication, publishing and education. What can science bloggers do to maximise their impact? Can blogging contribute to scientific research and careers? How can blogs be used to help educate the public about science? Readers and writers of science blogs, those who follow trends in online scientific communication and anyone else interested in learning more about science blogging will benefit from the discussions. You do not have to have a blog in order to attend.

This is just a recent example(2) of the growing role of blogging to communicate science, not just for popular reports but to communicate results between researchers. The immediacy and lack of a restrictive format fill in the gaps left by traditional journals. Key questions in the near future will continue to focus on how to quantify the contribution of blogging to an academic career.

Future of chemistry

Source

1) http://blogs.nature.com/nautilus/2008/05/science_blogging_conference_se_1.html
2) For other examples see: http://wiki.blogtogether.org/blogtogether/show/HomePage

People for the Ethical Treatment of Animals wants to pay a million dollars for fake meat

Rachel Maguire — Thu, 24 Apr 2008 12:30:37 -0700

Description

The idea of getting the next Chicken McNugget out of a test tube is not new. For several years, scientists have worked to develop technologies to grow tissue cultures that could be consumed like meat without the expense of land or feed and the disease potential of real meat. An international symposium on the topic was held this month in Norway. The tissue, once grown, could be shaped and given texture with the kinds of additives and structural agents that are now used to give products like soy burgers a more meaty texture.

New Harvest, a nonprofit organization formed to promote the field, says on its Web site, “Because meat substitutes are produced under controlled conditions impossible to maintain in traditional animal farms, they can be safer, more nutritious, less polluting and more humane than conventional meat.” The Netherlands has put $5 million into in vitro meat studies.

Jason Matheny, a doctoral student at Johns Hopkins University who formed New Harvest, said the idea of a prize for researchers was promising. Citing the example of the Ansari X Prize, a competition that produced the first privately financed human spacecraft, Mr. Matheny said, “they inspire more dollars spent on a research problem than the prize represents.”

Earth Systems & Environmental Science

Source

http://www.nytimes.com/2008/04/21/us/21meat.html?adxnnl=1&ref=science&adxnnlx=1209064885-88xYqLCdnEcJCC5HAgyWsQ