Chemistry Dept, ICSTM, Fax: +44 171 594 5804

Chemical Information Technology 2007-08

Six Lecture Demonstrations by Henry Rzepa
with individual practical sessions using a Computer

Department of Chemistry, Imperial College London.

Molecule needs Java 1.2

Checklist of items

  1. Location and time of Lectures: Friday 5 October 2006, 11am (Pippard), and Monday 8th October, 2pm (Pippard LT). Further lectures 11am-12.00 Tuesdays and Thursdays during weeks 2 and 3 (Pippard).
    Textbook: There is no course textbook, but the "Handbook of Chemoinformatics" (J. Gasteiger, Ed), Wiley, 2003, Vols 1-4, is the current definitive reference work.
  2. Relevance of this course: As of 5th October, 2007, there are:
    1. 32,648,792 molecules
    2. and 59,360,902 biosequences,
    3. undertaking 13,810,348 reactions, and
    4. for which there are 1 billion experimental properties
    5. described in about 10,000 journals and databases
    You can see that chemistry is a subject with a lot of finely-grained data describing it. Knowing about the appropriate tools for searching and handling such data, and transforming it into Information and knowledge is an essential part of modern chemistry. You will be introduced to the most important chemical information searching techniques, culminating in the requirement to put these techniques to good use in researching a specific topic as a project. In the second year, you will apply these techniques to laboratory course "unknowns" and to lab write-ups, for getting background to problem sets (indeed, even answers!), and later on for resolving specific questions relating to revision. Later in our course, you will have to do a "dissertation", which includes a much more in-depth analysis of a topical project, and a research project which will almost certainly also require researching. After you graduate, searching the chemical literature for information will become second nature to you if you continue in a chemical career.
  3. Login-IDs: You will require your local id, i.e. the one you use for e-mail and which should have been issued in your first year. Please ensure that you have this id and its password available for laboratory sessions. Some specialised databases may require their own id, which will be issued as required during lab courses.
  4. Presentation of Course: A set of Web pages linking access to chemical information sources. Some of these sources require pre-installed programs on the computer you are using, and a suitably configured Web Browser: we suggest using FireFox (on all platforms), one or two facilities may cause problems with Internet Explorer 6.0 (Windows only).
  5. Structure of the Course: 1) Managing your desktop and Office/EndNote, 2) 1D Bibliographic searches 3) 2D chemical structure searches 4) 3D chemical structure searches, 5) 4D Integrated information and added value environments.
  6. Lab Slots: Four allocated Lab sessions week starting Oct 8. Each student has two sessions in weeks 2 and 3 for either one of Monday and Thursday (Group A) OR Tuesday and Friday (Group B). Week 2,3 14.00-17.00 (Oct 8 only, 15.00-17.00). (12 hours)
    Further sessions are as follows:
    Group B will have week 4 (22 October) on Monday@14.00-17.00 and Thursday@14.00-17.00 (total time 18 hours).
    Group A will have week 8 (19 November) on Monday@14.00-17.00 and Thursday@14.00-17.00 = 6 hours (total time 18 hours).
    Please feel free to use either the Computer room OR the study area on level 2 outside of these hours. The latter area is NOT formally reserved and any student can use it at any time for this purpose if a computer is free. Students doing course and study work always have priority over students using the computers for non-chemistry related uses.
    Two demonstrators will be present during Weeks 2,3,4 and 8.
  7. Lab assignments: What to do in the first lab session and subsequent lab sessions.
  8. Assessment:There will be NO formal test at the end of the course. Instead, assessment will be via a wiki. This will contain approximately 20 article stubs modelled after a nascent wikipedia entry, with each containing a different molecule as the subject of the article. Your task will be to add content to these articles. For the rules of this game, see here. The status of the Wiki articles, and each individual's contribution to them by December 7th and no later, will be used for the project assessments.
  9. Plagiarism: Deliberately copying another person's (or pair's) work, or copying verbatim significant parts of another Web page is considered plagiarism. This can now be detected. Although we do not automaticaly invoke this process, we do reserve the right to subject your contributions to this test. The project should reflect your opinions (or jointly if a pair); you can quote a short length of text if you fully cite the source, and likewise diagrams. The continuum between citing other peoples work, and plagiarising it is however not absolutely clear cut ( see here for other people's opinions). To quote someone or other, whilst it may be difficult to define it, we all recognise it when we see it!

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