Chemotion ELN: an Open Source electronic lab notebook for chemists in academia

The development of an electronic lab notebook (ELN) for researchers working in the field of chemical sciences is presented. The web based application is available as an Open Source software that offers modern solutions for chemical researchers. The Chemotion ELN is equipped with the basic functionalities necessary for the acquisition and processing of chemical data, in particular the work with molecular structures and calculations based on molecular properties. The ELN supports planning, description, storage, and management for the routine work of organic chemists. It also provides tools for communicating and sharing the recorded research data among colleagues. Meeting the requirements of a state of the art research infrastructure, the ELN allows the search for molecules and reactions not only within the user’s data but also in conventional external sources as provided by SciFinder and PubChem. The presented development makes allowance for the growing dependency of scientific activity on the availability of digital information by providing Open Source instruments to record and reuse research data. The current version of the ELN has been using for over half of a year in our chemistry research group, serves as a common infrastructure for chemistry research and enables chemistry researchers to build their own databases of digital information as a prerequisite for the detailed, systematic investigation and evaluation of chemical reactions and mechanisms.

[1]  不破 博 ケミアブ訪問記 Chemical Abstracts Service , 1963 .

[2]  Thierry Laidboeur,et al.  Sanofi-Synthelabo Chemical Development and the Development of an Electronic Laboratory Notebook , 2004 .

[3]  Paul van Eikeren,et al.  Intelligent Electronic Laboratory Notebooks for Accelerated Organic Process R&D , 2004 .

[4]  Hilmar Lapp,et al.  Open source tools and toolkits for bioinformatics: significance, and where are we? , 2006, Briefings Bioinform..

[5]  Keith T Taylor The status of electronic laboratory notebooks for chemistry and biology. , 2006, Current opinion in drug discovery & development.

[6]  Luc Patiny,et al.  www.nmrdb.org: Resurrecting and processing NMR spectra on-line , 2008 .

[7]  Nigel H. Goddard,et al.  eCAT: Online electronic lab notebook for scientific research , 2009, Automated experimentation.

[8]  Data's shameful neglect. , 2009, Nature.

[9]  J. Ioannidis,et al.  Public Availability of Published Research Data in High-Impact Journals , 2011, PloS one.

[10]  H. Kitano,et al.  Software for systems biology: from tools to integrated platforms , 2011, Nature Reviews Genetics.

[11]  Michael Rubacha,et al.  A Review of Electronic Laboratory Notebooks Available in the Market Today , 2011, Journal of laboratory automation.

[12]  Jianing Zeng,et al.  Impact of the implementation of a well-designed electronic laboratory notebook on bioanalytical laboratory function. , 2011, Bioanalysis.

[13]  Michael Schneider,et al.  Going paperless: implementing an electronic laboratory notebook in a bioanalytical laboratory. , 2011, Bioanalysis.

[14]  Felix Rudolphi,et al.  Electronic Laboratory Notebook: The Academic Point of View , 2012, J. Chem. Inf. Model..

[15]  Clara D. Christ,et al.  Mining Electronic Laboratory Notebooks: Analysis, Retrosynthesis, and Reaction Based Enumeration , 2012, J. Chem. Inf. Model..

[16]  Christine L. Borgman,et al.  The conundrum of sharing research data , 2012, J. Assoc. Inf. Sci. Technol..

[17]  Wah Chiu,et al.  EMEN2: An Object Oriented Database and Electronic Lab Notebook , 2013, Microscopy and Microanalysis.

[18]  Jeremy G Frey,et al.  Laboratory notebooks in the digital era: the role of ELNs in record keeping for chemistry and other sciences. , 2013, Chemical Society reviews.

[19]  Jeremy G. Frey,et al.  First steps towards semantic descriptions of electronic laboratory notebook records , 2013, Journal of Cheminformatics.

[20]  James McKay,et al.  A universal open-source Electronic Laboratory Notebook , 2013, Bioinform..

[21]  Jeremy G Frey,et al.  Chemical information matters: an e-Research perspective on information and data sharing in the chemical sciences. , 2013, Chemical Society reviews.

[22]  Emily Walsh,et al.  Using Evernote as an Electronic Lab Notebook in a Translational Science Laboratory , 2013, Journal of laboratory automation.

[23]  Jeremy G. Frey,et al.  Sample management with the LabTrove ELN , 2014 .

[24]  Jeremy G. Frey,et al.  Creating Context for the Experiment Record. User-Defined Metadata: Investigations into Metadata Usage in the LabTrove ELN , 2014, J. Chem. Inf. Model..

[25]  Nicole Jung,et al.  Open source life science automation: Design of experiments and data acquisition via “dial-a-device” , 2015 .

[26]  Károly Héberger,et al.  Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations? , 2015, Journal of Cheminformatics.

[27]  Antony J. Williams,et al.  ChemTrove: Enabling a Generic ELN To Support Chemistry through the Use of Transferable Plug-ins and Online Data Sources , 2015, J. Chem. Inf. Model..

[28]  David Ryan Koes,et al.  Open source molecular modeling. , 2016, Journal of molecular graphics & modelling.

[29]  Brian Owens,et al.  Data sharing: Access all areas , 2016, Nature.

[30]  Piotr Dittwald,et al.  Computer-Assisted Synthetic Planning: The End of the Beginning. , 2016, Angewandte Chemie.

[31]  Bernd Rinn,et al.  openBIS ELN-LIMS: an open-source database for academic laboratories , 2015, Bioinform..

[32]  Declan Butler,et al.  Gates Foundation announces open-access publishing venture , 2017, Nature.

[33]  Kate Lawrence Open Access is Evolving and ChemistryOpen is Too! , 2017, ChemistryOpen.

[34]  Marwin H. S. Segler,et al.  Neural-Symbolic Machine Learning for Retrosynthesis and Reaction Prediction. , 2017, Chemistry.