http://precedings.nature.com/tags/Open%20Notebook%20Science Recently posted documents tagged with 'Open Notebook Science' Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://precedings.nature.com/documents/2237/version/1 The Ugi reaction has proved to be a convenient way to quickly create diverse libraries of compounds. It involves the reaction of an amine, an aldehyde, a carboxylic acid and an isonitrile typically in methanol at room temperature. The Ugi reaction has often been used as a tool in the synthesis of pharmacologically active molecules. It has been observed that Ugi products sometimes precipitate in pure form from the reaction mixture. This is a very fortunate outcome since the reaction can then be easily scaled up without requiring costly purification procedures such as chromatography. It would be most beneficial to optimize the Ugi product yield as obtained directly from filtering the reaction mixture without further treatment. To this end we utilized a 48-slot Mettler-Toledo MiniBlock equipped with filtration tubes. A Mettler-Toledo MiniMapper automated liquid handler was used to deliver the reagents and solvent. The parameters of interest were the concentration, the solvent composition and the excess of some of the reagents. This work was performed under Open Notebook Science conditions and links to relevant laboratory notebook pages are provided. http://precedings.nature.com/documents/2237/version/1 Fri, 29 Aug 2008 17:50:59 UTC Optimization of the Ugi reaction using parallel synthesis and automated liquid handling hdl:10101/npre.2008.2237.1 2008-08-29 Jean-Claude Bradley Nature Precedings 2008-08-29T17:50:59Z Manuscript Chemistry Pharmacology http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2008.2216.1 This talk was presented by Jean-Claude Bradley at the American Chemical Society meeting in Philadelphia on August 20, 2008. An introduction to Open Notebook Science is presented followed by an illustration of how ONS can be used in drug discovery. New data relating to the anti-malarial activity of Ugi products on 2 falcipain-2 docking sites is detailed. The docking calculations were provided by Rajarshi Guha and the enzyme and in vitro assays on Plasmodium falciparum were provided by Phil Rosenthal and Jiri Gut. Most of the syntheses were carried out by Khalid Mirza in the Bradley group.Screencast available at: http://video.google.com/videoplay?docid=3251406956070376532&hl=en http://dx.doi.org/10.1038/npre.2008.2216.1 Tue, 26 Aug 2008 17:09:10 UTC Open Notebook Science – Falcipain-2 Preliminary Results doi:10.1038/npre.2008.2216.1 2008-08-26 Jean-Claude Bradley Nature Precedings 2008-08-26T17:09:10Z Presentation Chemistry Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2008.1505.1 This is a pre-proposal written for the NSF program CDI (Cyber-Enabled Discovery and Innovation) in Jan 2008.The current system of dissemination of scientific data and knowledge is far less efficient than it needs to be to facilitate improved collaborative science, especially considering current publication vehicles and infrastructure. There is a growing movement promoting more Open Science with the belief that a more transparent scientific process can perform far more effectively. The logical extension of this concept is full transparency – exposing a researcher’s complete record of progress to the public in near real time. Not only will such a process enable ongoing data sharing it also provides an opportunity to develop collaborative communities of scientists and, at the conclusion of data acquisition, can enable communal extraction of conclusions when necessary. We have named this approach Open Notebook Science and have demonstrated its implementation and feasibility with the UsefulChem project, started in the summer of 2005, with the aim of synthesizing novel anti-malarial compounds. Our system currently uses free hosted services using general blog and wiki functions to facilitate replication across any scientific domains. These services are not chemically intelligent and are limited to text and graphic based data sharing only. For Open Notebook Chemistry the ability to intelligently manipulate, manage and search chemical structures and associated data is necessary and we have demonstrated proof of concept capabilities by integrating with the ChemSpider service, a free access online database managing chemical structures and focused on developing a structure centric community for chemists. This work will require the development of a chemically intelligent software platform to extend the capabilities of both the blog and the wiki environment for managing Open Notebook Science. The exposure of raw experimental procedures and data in a semantically rich format will enable the participation of both human and autonomous agents in the process of scientific discovery. This phenomenon of spontaneous group intelligence, referred to as “Crowdsourcing”, has proven valuable in several contexts. Already, productive collaborations have been forged within the UsefulChem project with groups from Indiana University, Nanyang Technological University, the National Cancer Institute and UC San Francisco. http://dx.doi.org/10.1038/npre.2008.1505.1 Thu, 10 Jan 2008 14:51:54 UTC Chemistry Crowdsourcing and Open Notebook Science doi:10.1038/npre.2008.1505.1 2008-04-08 Jean-Claude Bradley Nature Precedings 2008-01-10T14:51:54Z Manuscript Cancer Chemistry Bioinformatics http://creativecommons.org/licenses/by/3.0/