Drexel CoAS talks mp3 podcast

Jean-Claude Bradley presented on Open Notebook Science at the NIST Social Media Day on December 11, 2008. The talks starts with an overview of ONS and how it is being used to assess solubility measurements being crowdsourced in the ONS Challenge and Submeta Awards . The use of wikis, blogs, Google Spreadsheets, YouTube, Flickr, ChemSpider and other free hosted Web2.0 tools is highlighted. The UsefulChem project , involving the synthesis of anti-malarial agents, is then briefly covered. Finally, a very recent application of using Google Spreadsheets to automatically call web services to calculate volumes and weights of chemicals needed in reactions is demonstrated (code by Rajarshi Guha ).

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NIST Dec08 Open Notebook Science Talk

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update: transcript available

This talk covers Open Notebook Science from an information technology perspective. It was presented by Jean-Claude Bradley at the Drexel iSchool on November 11, 2008. Although solubility measurements and chemical reactions are mentioned the focus is more on how information is stored, retrieved and used using free and hosted services such as Blogger, GoogleDocs, Wikispaces, ChemSpider, CDD and others. The UsefulChem project and the Open Notebook Science Challenge are highlighted.

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iSchool Open Notebook Science Talk

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update: transcript is available

On October 10, 2008 Jean-Claude Bradley presented a 15 minute summary of Open Notebook Science and its application to the synthesis of anti-malarial compounds as part of a mini-symposium on faculty research in the Chemistry department at Drexel University.

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Open Notebook Science in 15 minutes

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This is a co-presentation by Jean-Claude Bradley and Andrew Lang on August 18, 2008 at the American Chemical Society conference in Philadelphia. The focus is on many of the tools available to easily demonstrate chemistry concepts in Second Life such as 3D molecules, reaction mechanisms, docking, organic chemistry quizzes, 5D graphs, the ACS museum featuring an HIV exhibit, the red tide phenomenon and many others. Most of the content on display rests on ACS island , Drexel Island and Nature's Second Nature island in Second Life .

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Bradley-Lang Chemistry in Second Life

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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.
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Open Notebook Science and Preliminary Falcipain-2 Results

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This talk was presented by Jean-Claude Bradley at the American Chemical Society meeting in Philadelphia on August 18, 2008.

This is an overview of how social media and Second Life can be used to productively network. Prominent recent examples involving Deepak Singh , Bora Zivkovic , Beth Ritter-Guth and others are highlighted. Then Second Life content that enables collaboration, especially in chemistry, is detailed. The presentation ends with an example of hyper-networking using FriendFeed followed by a few words from Andrew Lang from ORU and Sandy Adam from Sigma-Aldrich.

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Second Life and Social Media: Networking Gold Mine or Time Sink?

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This is a presentation by Jean-Claude Bradley at the Biennial Conference for Chemical Education (BCCE) on July 29, 2008. The talk starts with an overview of Open Notebook Science using a wiki as a public lab notebook. An example of the usefulness of publishing failed experiments is detailed, showing how the version history of the wiki can be used to track the evolution of an organic chemistry experiment. Near the end of the talk an example of using automation to optimize a Ugi reaction is mentioned.

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Open Notebook Science BCCE 2008

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I talked about Second Life in the chemistry classroom at the Chemical Heritage Foundation on April 29, 2008. This was part of the 8th Annual Leadership Initiative in Science Education (LISE 8 ). Most examples involve work done in collaboration with Andrew Lang. At the end I invite the group to an in-world meeting on May 6, 2008 at 13:30 EDT on ACS island. (slurl )

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I present on using Second Life to teach chemistry at the American Chemical Society meeting in New Orleans April 7, 2008. Examples include using quizzes, generating 3D molecules, visualizing docking, proteins and reactions. An overview of ACS island is also given, with a focus on the Sci-Mix virtual poster session. Much of this work was done in collaboration with Andrew Lang.

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Jean-Claude Bradley presents on "Open Notebook Science: Putting the Information User in Control through Transparency" at the NFAIS meeting in Philadelphia on February 24, 2008. This was part of the session on "The Emerging Culture of the New Information Order". The use of public blogs, wikis, GoogleDocs and mailing lists to conduct research on the synthesis of new anti-malarial agents is described.

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I spoke at the North Carolina Science Blogging Conference (un-conference really) on January 19, 2008. Mainly I reviewed some of my posts on the UsefulChem blog from the past few months to show what types of issues are relevant to doing research openly. I then showed the connection from the blog to the wiki, mailing list and GoogleDocs where the laboratory data get reported and analyzed.

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My co-presenter Xan Gregg's talk screencast (SciVee)

On November 27, 2007 I presented our work on Open Notebook Science . I had a little more time to explain most aspects of our work to a scientific, but not necessarily a chemistry audience.

Near the end I did discuss some of our very recent results relating to our CombiUgi project and the synthesis of some compounds about to to be tested for the inhibition of the malarial parasite's enzyme Falcipain-2 .

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A Beginner’s Guide to Open Science(not for beginners but by beginners)
A talk by Cameron Neylon
STFC Rutherford Appleton Laboratory and School of Chemistry, University of Southampton

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Update: transcript is now available

Presentation at 2:00 Friday November 2, 2007
Disque 109, Drexel University

The modern biochemistry or molecular biology laboratory generates large quantities of data that are generally stored across multiple computers attached to multiple instruments. Much of this data is never published and the majority languishes on old computers and is ultimately lost. At a local level this is a frustration for investigators who will often struggle to obtain specific pieces of data produced in their own laboratory. On a larger scale this is becoming a much more serious issue with the obligation of researchers to funding bodies to both preserve research data and make it available to other users increasingly becoming a formal a condition of publicly funded grants. Systems are required that can capture and preserve data along with sufficient information and metadata to make it possible for others to use this data.

In parallel with this a movement is growing within the research community that advocates greater openness in providing both the raw data from published studies as well as making available the large quantities of data that are never published. The logical extreme of this approach is Open Notebook Science [1], pioneered at Drexel University [2], where the researcher’s laboratory notebook is made available on the internet as it is recorded. Achieving the aims of Open Notebook Science also requires systems which can capture data and provide it in a useful format. In addition these systems must make the data visible to relevant online searches.

We are developing and using an electronic laboratory notebook based on a Blog format to capture experimental data in a biochemistry laboratory [3,4]. Within the system each sample is recorded in a single post. Analysis and manipulations of the sample are recorded in separate posts with links back to the input sample and forward to any products. All the information is made immediately available on the Web as it is recorded. The Blog engine has been specially built in house and has a number of features designed to enable and encourage the effective capture of data and metadata in the environment of a biochemistry laboratory. I will describe the Blog system and our evolving approach to capturing metadata as well as the process of integrating this with other web services to provide an open environment for recording work in the laboratory, laboratory materials, and validated procedures. The challenges and problems encountered in reconciling the twin aims of capturing data and making it available and readable will also be discussed along with the similarities and differences emerging between different approaches to Open Notebook Science [2,5,6].

[1] http://drexel-coas-elearning.blogspot.com/2006/09/open-notebook-science.html
[2] http://usefulchem.wikispaces.com/
[3] http://chemtools.chem.soton.ac.uk/projects/blog/blogs.php/blog_id/10
[4] http://chemtools.chem.soton.ac.uk/projects/blog/blogs.php/blog_id/13
[5] http://www.jeremiahfaith.com/open_notebook_science/
[6] http://www.michaelbarton.me.uk/

Bill Erb's thesis defense on June 12, 2007 at the Drexel University Chemistry Department.

Exploration of the Fundamentals of Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry

This thesis focuses on the study of different tools that can be used for preparing samples for matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOFMS) and utilizing these tools to study different ionization processes that are operating in the MALDI experiment.

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This is my April 19, 2007 presentation at the British Columbia Library Association Conference on Open Access. There was only time to do a brief introduction about trends in openness in education and research and how that might affect the needs of scientists in publishing and finding information. I also showed a few screenshots of UsefulChem near the end.

Thanks to Heather Morrison for the invitation!

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Here is my talk "Open Notebook Science using Blogs and Wikis" at the American Chemical Society meeting in Chicago on March 27, 2007 at the Communicating Chemistry Symposium.

The first half is basically a condensed summary of how we are using UsefulChem to do Open Science. I then demonstrate for the first time Dave's Excel code to compute kinetics from JCAMP NMR reaction profiles and the building in Second Life where Beth and Eloise have help me to set up a poster room with NMR spectra, molecules and an organic chemistry quiz .

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Where is technology most effective: inside or outside of the classroom?
Dan King, Drexel University

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Philadelphia Area Educational Technology Conference Feb 23, 2007
At Drexel University, environmental chemistry is taught to a diverse group of students in a single class. The student population includes both upper level undergraduates and beginning graduate students from a variety of majors. The preparation level of these populations is quite variable, as many of the graduate students have not had a chemistry course in several years. Consequently, a significant amount of time must be spent reviewing fundamental chemical concepts. These general concepts are either incorporated into the lecture material or reviewed in group activities. Two forms of technology were used to improve student learning. In class, personal response systems (or “clickers”) were used to reinforce the lecture material. Outside of class, students use an online discussion board to post questions related to homework problems. The Student Assessment of Learning Gains (SALG) survey was used to help identify which components of the course helped the students learn the material. These results will be compared to end-of-term evaluations and measures of student performance during the term.

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iTunes U Implementation
Brian Gall and Russ Pritchard, Philadelphia University

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Philadelphia Area Educational Technology Conference Feb 23, 2007

Philadelphia University has implemented a new hosting solution for its educational audio and video content. Learn how we implemented the iTunes University Podcasting solution to create a collaborative learning and information space for the administration, faculty, students and learning community.

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Don't Make Me Think - I'm Here to Learn
Mike Zarro, Drexel University

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Philadelphia Area Educational Technology Conference Feb 23, 2007

3.2 million people took at least one class online in the fall of 2005. As a student in Drexel University's online Master of Library Science program and a webmaster for 8+ years, I'll share my experiences and observations of eLearning success and areas of improvement. Online education more than just Blackboard - it includes video, podcasts, and online collaborative workspaces.

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