Jeffery Loo – UC Berkeley

Here is the workbook for an instructional session on finding inorganic chemical information.

Download a PDF copy of the workbook.

This is the second year of teaching this class and we now cover Reaxys instead of Gmelin and have a more detailed exploration of Boolean operators. There were 2 separate sessions – each 4 hours long – for a total of 11 students.

Please download a copy here.

Background
POGIL is short for Process Oriented Guided Inquiry Learning.  Its basic tenets are:

• Instruction can teach content as well as process skills like analytical thinking and effective teamwork.
• Students collaborate in teams and work through guided learning activities.
• Leading questions are posed to students.  By following a number of guided activities, students find answers to the questions and formulate validated conclusions.
• The instructor serves as a facilitator, addressing individual and group needs, while students work in self-managed teams.
• The POGIL project is supported by the National Science Foundation and the U.S. Department of Education, among other groups.
• (Paraphrased from: http://pogil.org/about)

Purpose
In UC Berkeley’s Chemistry 108 (Inorganic Synthesis Laboratory), students write lab reports that require references to chemical literature.  To help students with this assignment, the Chemistry and Chemical Engineering Library provided a 3-hour instructional session that explained:

• Types of chemical information resources including tertiary, secondary, and primary resources
• When to use information resources in scientific writing
• Preparing reference citations in ACS style
• Searching by chemical structure, molecular formula, and name
• Searching SciFinder, Gmelin, and Combined Chemical Dictionary
• Learning about the history of a research topic/article and its later development via cited reference searches
• Finding information resources at the Chemistry and Chemical Engineering Library
• Availability of ChemDraw and bibliographic software to aid scientific writing

Methods
A POGIL-inspired approach was taken for the Chemistry 108 library instruction.

• A “libratory” manual was created with short, guided activities that help students understand information literacy concepts, recognize information research problems, and then resolve them through hands-on searching of databases.
• Students worked in groups of 2 or 3 to search chemical information databases together.
• After each short activity, our class engaged in a group discussion of the learning outcomes and any questions raised.

Results

• Two classes were taught:
  • September 8, 2010 –  8 students (3 hours)
  • September 9, 2010 – 6 students (3 hours)
• A “libratory” manual with guided activities and post-activity discussion notes was prepared.
  • Please download here.

11 more videos available at

http://www.jeffloo.com/stuff/2010/instruction/pubchem/

PURPOSE: To make online instructional videos for PubChem, a free database of the biological activities of small molecules developed by NCBI at the National Institutes of Health.

METHODS: Develop modular videos that address research problems and tasks in chemical informatics. This arrangement encourages remixing, reuse, and sharing that can be tailored to different learning needs. The videos are stored in and delivered through YouTube – a popular, video-sharing website that offers social media features for commenting, voting, and video sharing.

This pilot project demonstrates that online video development is not cost prohibitive when using software and services that are free, open source, readily available at academic libraries, or cost five dollars.

For details of why and how these videos were developed, please visit:

http://www.jeffloo.com/stuff/2010/instruction/video/

RESULTS:
Twelve instructional videos were developed.  Some topics include:

• Searching PubChem
• Understanding, simplifying, and saving search results
• Searching and downloading chemical structures
• Searching for and viewing bioactivity data
• Viewing 3D chemical structures
• Conducting a structure-activity analysis
• and more!

See all  videos at either:

http://www.lib.berkeley.edu/CHEM/instruction/pubchem/
or
http://www.jeffloo.com/stuff/2010/instruction/pubchem/

TYPE: Seminar

METHODS: Initiated, organized, and promoted the seminar.

SPEAKER: Dr. Antony Williams.  He is the Vice President of Strategic Development at the Royal Society of Chemistry and is the host of ChemSpider, a free online structure centric community for chemists.

AUDIENCE: Lawrence Berkeley National Laboratory, UC Berkeley personnel, and researchers interested in online collaboration, data storage and curation, data exchange, crowdsourcing, and open access.

FORMAT: 90 minute presentation

DATE AND VENUE: March 24, 2010 – Building 50 Auditorium, Lawrence Berkeley National Laboratory

ABSTRACT: The increasing availability of free and open access resources for scientists on the internet presents us with a revolution in data availability. The Royal Society of Chemistry hosts ChemSpider, a free access website for chemists built with the intention of building community for chemists (http://www.chemspider.com/).

ChemSpider is an aggregator of chemistry related information, at present over 20 million unique chemical entities linked out to over 300 separate data sources, ChemSpider has taken on the task of both robotically and manually curating publicly available data sources. It is also a public deposition platform where chemists can deposit their own data including novel structures, analytical data, synthesis procedures and host data associated with the growing activities associated with Open Notebook Science.

This presentation will examine chemistry on the internet, the dubious quality of what is available and how the ChemSpider crowdsourced curation platform is fast becoming one of the centralized hubs for resourcing information about chemical entities.

We will also review our efforts to provide free resources for synthesis procedures, spectral data and structure-based searching of the chemistry literature and how chemists can contribute directly to each of these projects.

Following the presentation and a question and answer session, a hands on session showing how to search for, curate and deposit data on ChemSpider will be given for interested parties.

SCREENCAST:

SLIDES:

PURPOSE: To identify academic programming models for chemical informatics and draft plans for the Chemistry and Chemical Engineering Library at UC Berkeley.

METHOD: Reviewed chemical informatics programming at academic and government institutions. Prepared a summary report and drafted preliminary plans for the library.

REPORT: Full text PDF

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