Open source laboratory data: Small-scale management

Open molecules

The management of chemical structures in a small laboratory is an important and often tedious daily task. Proprietary software is costly and by definition closed, but an open source modifiable and redistributable application, MyMolDB, could make life easier for small lab managers.

Bing Xia, Zheng-Fu Tai, Bang-Jing Li, Li-Sheng Ding and Yan Zhou of the Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, at the Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu and Yu-Cheng Gu of Syngenta's Jealott's Hill International Research Centre, in Bracknell, Berkshire, England report details in the Journal of Computational Chemistry.

The team describes MyMolDB as, "a micromolecular database solution that supports exact, substructure, similarity, and combined searching." It is implemented mainly using the scripting language Python and has a web-based interface for compound management and searching. The software circumvents the problems of currently available open-source applications that are typically of limited functionality when it comes to basic cheminformatics, the team says. The developers add that searches are done with pure SQL on the database by using the high performance of the database engine and so offer impressive search speeds even on large data sets but side-step the problem of the excessive consumption of Central Processing Unit cycles.

Over the centuries, scientists have produced literally millions of chemicals. On 20th May 2011, the CAS Registry announced its 60 millionth entry, a number that had grown by 10 million since 2009 and at the time of writing (mid-July 2011) had grown to 61,369,479. Every page refresh of the CAS website adds a handful more. That vast database doesn't even begin to take into account proprietary databases or combinatorial repositories or the private databases being used by countless small laboratories.

Traditional options

Traditionally, the smaller lab might use a spreadsheet to keep track of the small molecules that are of interest to its scientists. It might even have turned to commercial products from the likes of Chemaxon or CambridgeSoft or an open-source program such as Haider. "These solutions have their particular merits," the team explains. "For the commercial ones, they have their advantages when it comes to handling very large numbers of data sets, whereas for the open-source ones, they are free in most cases, and their source code is open, so you can add your own functions into them at your will if you are familiar with related programming language."

For a small laboratory, there are cheminformatics requirements that usually amount to databases of a few thousand or a few tens of thousands. The large-scale commercial applications may be too unwieldy or simply too expensive, whereas the open source applications often have too many limitations for diverse studies. The team has developed MyMolDB as an open source application that can handle up to a million compounds.

Chemistry on the web

"The web-based searching pages provided user- friendly human-computer interface for compound searching and user management. The Python-based essence grants the extensibility of this system. We provided the libraries within the package which can be used for further extend on cheminformatics-related functionalities," the team says. The researchers add that they are currently developing a plug-in system and are inviting developers to participate via the Google Code site for the project - http://code.google.com/p/mymoldb.