Mirza PhD defense on the Ugi reaction for anti-malarial screening

submitted by: jcbradley
Khalid Baig Mirza defends his Ph.D. thesis at Drexel University on December 6, 2010 (advisor JC Bradley). He first discusses Open Notebook Science and his contribution to the sodium hydride oxidation controversy. Then he describes the UsefulChem project, involving the use of the Ugi reaction as an approach to synthesizing new anti-malarial agents, including a few unexpected side reactions and challenges. Finally he presents an overview of the ONS Solubility Challenge and its application to...

OpenSciNY Open Notebook Science Talk

submitted by: jcbradley
On May 14, 2010 Jean-Claude Bradley presented on Open Notebook Science at the OpenSciNY conference at the New York University Library. He introduced the topic by telling a few stories about how new forms of communication are affecting how we think about concepts like "scientific precedent", "peer review", "scientific publishing" and "scientific scholarship". At the end he spoke about archiving Open Notebook Science projects culminating in the publication of the Reaction Attempts and ONS...

Cheminfo Retrieval Class 8th FA09

submitted by: jcbradley
This is the lecture from the 8th Chemical Information Retrieval class at Drexel University on November 12, 2009. It starts with a demonstration of how to use of ChemSketch and Chemspider to display and manipulate chemical structures, especially those with complicated stereochemistry. Technical issues with using SMILES between the two platforms are addressed, as are optimization of 3D structures and inverting chiral centers. Microsoft Paint is used to process screen captures to images that...

Cheminfo Retrieval Class Six FA09

submitted by: jcbradley
This is the lecture from the sixth Chemical Information Retrieval class at Drexel University on October 29, 2009. It starts with a review of some of the new questions answered by students from the chemistry publishing FAQ, which covers patent information and accessing electronic journals at Drexel. Tony Williams submitted a puzzle to resolve conflicting structures in ChemSpider, which is too difficult to be a regular assignment. It requires re-analyzing spectroscopic data in papers where...

Cheminfo Retrieval Fourth Class FA09

submitted by: jcbradley
This is a recording of the fourth class on Chemical Information Retrieval on Oct 15, 2009 at Drexel University. It starts with some tips on removing formatting from Wikispaces pages, the Drexel Cisco VPN client for accessing paid subscriptions off campus and how to link to a DOI. The first two assignments for the class are then described. The first involves summarizing each paragraph of an article and an option to use AcaWiki is demonstrated. The second involves filling in an FAQ for...

NERM 09: Leveraging Transparency and Crowdsourcing in Chemistry Using Open Notebook Science

submitted by: jcbradley
Jean-Claude Bradley presents on October 9, 2009 at the Northeastern Regional Meeting of the American Chemical Society in Hartford. This talk, entitled "Leveraging Transparency and Crowdsourcing in Chemistry Using Open Notebook Science", was part of a symposium on Publishing and Promoting Chemistry in the Internet Age. It consists of an overview of Open Notebook Science with some new content on solubility prediction algorithms written by Andrew Lang and a few example of students taking a...

Structural Bioinformatics Pharm 201 UCSD Lecture 3

submitted by: Phil

This is lecture 3 from a graduate student class in structural bioinformatics offered at UCSD

Using social networking tools a la carte for organic chemistry education: wikis, blogs, Second Life, and more

submitted by: jcbradley
Jean-Claude Bradley describes the use of social networking tools to teach undergraduate organic chemistry. Public free wikis can be used effectively to manage class information as well as serve as a versatile platforms to process student assignments and provide rapid feedback. Examples of using Second Life to deliver quizzes, play games and offer students an environment to create projects involving 3D molecules, spectra and posters are detailed. The continuously evolving role of blogs,...

The Spectral Game: Learning spectroscopy using open data

submitted by: jcbradley
Jean-Claude Bradley presents on the Spectral Game at the American Chemical Society meeting in Washington, DC on August 17, 2009. The talk provides an overview of how openness in both teaching and research can help generate new educational resources, especially for teaching NMR. At the end Antony Williams says a few words about the Spectral Game project and the ChemSpider database which powers it via Open Data JCAMP-DX spectral depositions. The other developers of the game are Andrew Lang...

Crowdsourcing Solubility using Open Notebook Science

submitted by: jcbradley
Jean-Claude Bradley presents at the American Chemical Society on August 16, 2009. The talk starts with highlighting how Open Notebook Science has been used to shed light on the recent report of using sodium hydride (NaH) as an oxidant. Next the Open Notebook Science Challenge is described, where ONS coupled to crowdsourcing is used to measure and share non-aqueous solubility data. Recent developments in using bots to contribute to the scientific process and applications to the Ugi...