It:coursework-2011

From ChemWiki
Revision as of 13:43, 20 July 2011 by Amckinle (Talk | contribs) (→‎Lecture Support: A SciFinder search instead)

Jump to: navigation, search

Go to Introduction | Go to Lectures | Go to Coursework | Go to Assignment

Overall Objectives of CIT workshops

The Computer lab is (<PDF LINK> formally booked for your group, A1, A2, B1, B2) for your course work and you have priority over other users at these times. You are of course free to use the computers outside these times for course work, but on a first-come-first served basis and only if another course is not running. You can also use the computers located in the study area and you have access to 24 hour opening in the central library, although you may find not all of the chemistry-related programs will be available there. During the lab time allocated for the IT course (two sessions in one week for each group, and one final session), you will be expected to achieve the following objectives:

  1. Accessing course and laboratory notes and using scientific journals to support lectures
  2. Using Word in combination with the EndNote bibliographic database and ChemDraw to write laboratory reports and essays
  3. Various bibliographic chemistry search systems
  4. Various molecular structure based search systems
  5. Applying these searches to the requirements of a laboratory course

You should of course appreciate that the distinction between lectures and labs is rather artificial, and any database which you might use for one is certainly useful for the other as well.

Software Familiarity

There are a number of programs with which you will use throughout your study at Imperial College, and the aim of these sessions is to give you an introduction to some of the packages, as well as explaining what the other packages do. In order to gain the most from your two workshop sessions, you are urged to complete the following section before you come to the workshop sessions:

Before you come to the workshop sessions...

...there are a few exercises you should perform to ensure you are familiar with the operation of the computer systems available on campus.

  • Check your login works; if you are browsing on a campus computer, then you will have already logged in. If you are accessing from your own computer, ensure that you can sign into your campus email account through the web interface.
  • Using the FireFox web browser (Firefox is better at handling chemistry search packages than Internet Explorer, and can be more reliable especially when running Java applets), you should be browsing this ChemWiki (home page URL of ChemWiki: http://www.ch.ic.ac.uk/wiki/). It should be listed in the Bookmarks menu of department cluster computers; you may wish to add it to the bookmarks of your own computer also.
  • You will be using Firefox to browse the pages of a Wiki. There is only one suggestion for browsing these pages that you might wish to follow. When encountering a hyperlink, as in the preceding link describing what a Wiki is, you will probably want to open it in a separate window or tab from the instruction page (so that you can refer to both if the need arises). If you just click the link, it will replace the instruction window. So, get used to clicking on the link with the right mouse button rather than the left one. This will then give you the option of opening the link in either a new window or a new tab of the current window.

Computer, Browser and Wordprocessor familiarity

  • login window
    Log-in. There is one important difference between using a home computer and the ones here; you need to authenticate your session with the password issued to you at registration. Check the login window looks as shown on the right, and proceed to login.
  • Document home
    Perhaps the single most confusing aspect for most people is what the Home icon (left) means. So let's sort this out immediately. You are working in an enterprise environment, where a fast network connects each computer to a central area for storing files. When you log in, you are granted access to your files, and on the computer desktop, the Home icon means "the directory where the folders and documents associated specifically with the login account are stored". This is because all computers work on the metaphor of a filing system with hierarchies. Home is the top of your personal file system! If you double click this icon, you should see YOUR files. Check this! If you get lost navigating the hierarchical directories, "Home" is always a useful way of restoring a sense of orientation. Home also has a synonym, called "My Documents", which the operating system can sometimes display instead of Home.
  • Office 2007
    Subs and Superscripts
    EndNote tab
    Start Microsoft Office 2007 (we will assume you still have FireFox running). The basic (Home) Word document work area is shown to the in the thumnail to the right (click to expand it) and you should familiarise yourself with some of the palettes. This version of the program is somewhat different from earlier versions you may already be familiar with, such as Office 2003. In particular, open/save/print dialogs are now to be found by pressing on the Icon highlighted here with a red circle. Copy/paste operations are invoked using the icon encircled in purple. Other common operations are found to the right of these two in the taskbar, including the chemically useful subscript and superscripts (right diagram). Note also the the default document saves invokes the new .docx format, which is an XML-based type with much interesting informatics potential. If you intend sending a document to someone who is still using Word 2003 or earlier, you should instead save your document in the older .doc format (although .doc to .docx converters are available). You can also save as PDF, which is useful for project/report submission.
  • Insert tab
    There are two other task-bars you will find useful. the Insert bar inserts a variety of other content, including pictures, tables and the like. The EndNote tab invokes a citation and reference manager, which you will use as described below (Important: If the Endnote ribbon does not show, do the following; Go to Programs/Additional Programs/EndNote/Configure EndNote and run this script, whereupon the EndNote ribbon should appear in Word 2007).
  • Practice copying text from the Firefox Browser Window to the Word document. You can do this using the Copy/Paste metaphor, or you can try the drag-n-drop mode. You will notice that whilst the text itself comes over, any formatting associated with this text (size, colour, weight etc) might not. You may also get more than you bargained for (i.e. hidden browser instructions etc.) [This copy is a one-way operation, since the FireFox window is "read-only"].
  • Save Firefox image
    Images are special when it comes to copying. Proceed as follows:
    1. Find an image in the browser you wish to copy, and with the cursor over the top, right click (Windows) to get a menu that looks like the one on the right:
    2. If one of the options is Copy image, select it. Not all browsers support this, in which case instead invoke save this image as and save it in an appropriate directory (A suitable sub-directory of Home on Windows).
    3. With an Office Word window open, paste the image (if you copied it) or Insert/Picture/from file (if you saved it). The image will come over as its "real size". Word will allow you to rescale it, by dragging the bottom right corner of the image. Observe carefully what happens if you resize it to be larger as well as smaller.
    4. Do remember how to change between windows (the technical term is that the active window is said to be on focus) by selecting the required window from its icon shown on the task bar/dock at the bottom of the screen.
Pentahelicene
 Not everything is always "copyable". Some apparent images are in fact produced by an "applet" embedded in the browser. This includes most conspicuously chemical diagrams, such as may often be found on these course notes. Here a copy or a save operation may not produce the effect you desire.
  • Practice naming and saving document files to your Home (Drive H: on Windows) or a removable medium such as a FlashDrive.
  • Practice finding files and documents from these various locations. [It frequently happens that they do not get saved where you think, and finding such lost files is skill you need to acquire rapidly!] Note however that finding content of files may be very slow. Windows Desktop Search is NOT activated on College systems.
  • Practice setting up E-mail, sending a document as an attachment (to yourself) and good e-mail housekeeping and etiquette.

Configuring storage for your document libraries

Programs such as EndNote, Mendeley, iTunes store document collections in the form of libraries. These can get quite big over the course of time, and so its important to store them correctly.

EndNote

When you open EndNote for the first time, it will offer the opportunity to create a new library. You should save it in the location e.g. Computer => userid(\\icfs18.cc.ic.ac.uk) (M:) Thereafter you can set it to open this library when the program starts.

Mendeley

Open the program and invoke Tools/Options/File Organiser and select drive M: for the library.

iTunes

Use Edit/Preferences/Advanced and set the iTunes Media folder location to M: (or other if M: is already full). Also tick Copy files to iTunes Media folder when adding to library.

You may find it advantageous to start working through the Workshop material below in advance of your scheduled workshop as it will allow you to identify any problem areas upon which you can concentrate with a demonstrator.

Start of Workshop material

The material which follows is intended to be the start of what is covered in the workshops and for which support will be available. This does not mean that the work cannot be done outside of the allocated workshop time; in fact you are positively encouraged to continue working through the material at your leisure. The notes here are intended to be a continuous point of reference throughout your course as you will continue to use many of these software packages for the next 3-5 years at least!

Combined Word/ EndNote Familiarity

This section will illustrate how the functionality of Word can be extended using a citation or reference manager. First, you will need to generate some citations, and this will be done using a database known as Web of Science, and with the objective of finding out a about penicillin and its conversion to cephalosporin.

A Web of Science Search

  1. WoS search
    From the Web-of-Science link (which you are advised to open in a separate window, using a right-click from the mouse), select the option to
  2. Connect to the ISI Web of Knowledge Service and then select the
  3. Web of Science tab from along the top and finally from the citation databases, narrow it down to the
  4. Science Citation Index expanded
  5. Try checking on the number of articles members of our staff (or your tutors) published in 2009 by entering their name into the Author box. You almost certainly will need to know that first, and probably also their second initial for this to correctly identify them. Check its working by entering a string in the advanced search such as au=Spivey a* and og=imperial and py=2001-2010 and SO=(CHEMICAL COMMUNICATIONS)
  6. When you have some hits, either tick individual citations, or All records on page or a span of records.
  7. Next, make sure you have Microsoft Word running, and from the EndNote X4 taskbar of Word, click on Go to EndNote. From the options offered (which you only see the first time you run EndNote, and also, ignore prompts about EndNote Web for the time being), create a new EndNote database, currently of course empty.
  8. saving a list for Endnote
    Return to the Browser window displaying WOS and click on Save to EndNote. An automated procedure should initiate, the end result of which will be that your EndNote library will now be populated by the references you have just found.
  9. If the automated procedure does not initiate, the system will instead produce a file on your computer desktop (it may appear with the name uml_view.cgi on the desktop) which you can open directly with EndNote (see below).

Inserting the citations just found into Word using EndNote

  1. Starting EndNote
    Go back to your bibliographic library in EndNote and before anything happens to it, save it to your M: drive as described above.
  2. Via Edit/preferences/Libraries select to load this database upon startup, thus dispensing with subsequent startup dialogs (it will in fact default to opening the most recently used library).
  3. Checking the style setting
    From Edit/Output style/Open Style Mananger, select the tick-box against a template known as Royal Society of Chemistry (you may have to use Find by/Chemistry to locate it). From now on, always check that this style is correctly set when you open EndNote (arrow 1 to the left).
  4. If you are importing a citation list rather than relying on the automated procedure, then from File/Import of EndNote define the Import Option ISI-CE in the pull down menu, or Other Filters/SciFinder (CAS) if importing SciFinder Scholar) and import any saved datasets you created earlier from WOS or SciFinder.
  5. Endnote1c.jpg
    Endnote1d.jpg
    Go back to Word 2007, and write some text. At an appropriate point, from the Endnote X4 taskbar tab, press Go to EndNote when your library should be revealed (in this case containing the references you have just imported). Select the one you want to insert, and press the Insert citation tab (arrow 2 to the left). If everything has been set up correctly, Word should insert your desired reference from your bibliographic database, formatted according to the RSC guidelines. If you rearrange the order in which the references appear in the text by cutting/pasting, the numbering at the bottom should change accordingly. If you delete a reference, it should disappear from the numbered list.
  6. Save the Word document for future reference. It should serve to illustrate how you will write lab reports, and later in your degree, extended essays (where you may cite between 50-100 references). The whole point of doing it this way is that all the otherwise arduous tasks of numbering and editing the references will be automated for you.

Mendeley and other alternatives to EndNote

Refworks.jpg
A significant problem with EndNote is the cost. This does not matter whilst you are using computers within the College, but it does matter if you want to use your own computer. Alternatives to using EndNote as shown above include RefWorks (for which the client software can be downloaded without cost) and an innovative program called Mendeley which is available on the computers in the department.
  1. If you do want to use RefWorks, please ensure you login via the Shibboleth users option.

Chemdraw Familiarity

  • Click to expand image
    Taxol
    Starting and using ChemDraw. Start Chemdraw icon from the Start/Programs menu. Practice by drawing Taxol (right). You many need a few hints and tips, and the demonstrators should be able to help you with this. Its easier than trying to describe the technique here (don't worry, everyone picks up Chemdraw by watching others use it!).
  • Check that you have drawn it correctly by calculating its formula. To do this, Go to View/Show analysis window and record what you see (it should give you C47H51NO14. Mol. Weight 853.91). Do you get the same values? If you do not, you will have to try to find where the discrepancy is. Remember, if you cannot draw a structure reliably, you will not be able to search for it reliably. Using the ChemDraw application, select copy/paste the structure into a Microsoft Word window. Practice editing the structure inside the Word processor by double clicking its diagram. Practice re-scaling the ChemDraw diagram either within Word or within Chemdraw. Scaling is normally done by pointing the cursor at the bottom right hand corner (it should change shape at this point) and then "dragging" inwards or outwards to change the size. Try copying instead the Web picture (GIF format) from this Web page to Word. Put side by side with the picture of the same molecule derived from ChemDraw and experiment with scaling both. What is the difference in behaviour?

If you want more practice (with stereochemical wedges text positioning, etc), try the molecule on the left. Can you identify what it is called?

Lecture Support: Journal Familiarity

You can go visit the home pages of some major chemistry publishers, and track down any articles that members of this department may have published there. You might try searching for your current lecturer, or one or more of your tutors. Go directly to one or more of the following

The navigation of these journals via their tables of contents is left for you to explore on your own. You can of course go to an article directly by following any DOI link that you might have found in your lecture notes or elsewhere. You should retrieve the Acrobat file corresponding to any articles you may have tracked down, and save them in a folder on your computer H: drive for future use and analysis (for example with the program Mendeley). Later in your course, you may encounter lecture courses or laboratory courses which in fact require you to track down articles in the literature in this manner. It is good to start practising early.

Lecture Support: Named chemicals

  1. To apply the above skills by using WOS to perform a comprehensive literature search on the molecule Penicillin, a reaction (its conversion to Cephalosporin), its properties, both physical (spectroscopic) and biological. Thus, type penicillin and cephalosporin into the Topic box and see if you can prune these down with a more elaborate search perhaps, using some of the Boolean logic shown in the lectures by invoking the Advanced Search option.
    • TI=Reaction AND (TI=penicillin OR TI=cephalosporin) (136)
    • (TI=Reaction AND TI=Penicillin) OR Ti=cephalosporin (2629)
    1. Or, try the drug Temozolomide, currently very much in the news
    2. Tasimelteon (time bending drug for jet lag) or
    3. Sulforapane, which occurs in broccoli and cauliflower and protects against heart attacks.
  2. Compare the results of one of these searches with less specialised search engines such as

Lecture Support: A SciFinder search instead

  • The Scifinder Scholar system has seven licenses for general and student use. If you are lucky enough to connect (which means getting up early, staying late or working on the weekend), proceed as follows
    • You cannot use your College login for access, but must request your own login to be created.
      • Go here to register. You have to create yourself a login ID. This ID is quite independent of your College ID, and if you forget the password you have set, you will have to recover it from the SciFinder site. Where it asks you to identify your area of research interest, you may not want to reveal this (we have been assured students will not get related spam sent to them) and you might want to register an interest only in e.g. other field.
    • Completing the registration will result in an email being sent to the email address you provide with activation instructions.
      • Once you have obtained an ID, at the SciFinder site, click on Explore References and in the Research topic box enter "Conversion of penicillin to cephalosporin".
    • You will receive a request to accept an application digital signature at this stage, which you should accept.

You should get ~9 references for an exact match. This interface is supposed to use a more natural language for its search queries (and it does not employ Booleans).

    • Tick the box with 9 hits and request the references. Tick the box against those you particularly wish to save for the future, and then click on the Export link near the top (next to print). From the dialog, set the File Type to Tagged Format.
      • You may need to allow the requested security settings in your browser (IE 8) to allow files to be saved locally. The default location for saving files is your download location. You can then import this into EndNote using the SciFinder (CAS) import option.
    • An alternative search might be the phrase arrow pushing formalism (can you learn about this topic from the results found for this search?). A synonym might be curly arrow formalism. Does this find the same references, or a different set?
    • You can comment on individual references and invite friends in to see your comments. This might be appropriate for when you are e.g. doing a lab experiment in pairs or groups, and wish to share a reference with them. Go to My connections and invite the group, then add comments to relevant references.
    • SciFinder supports more advanced features such as Explore Substances and Explore Reactions, but you should only investigate these when you are feeling adventurous.

Laboratory Support

Continuation of CIT skills

Retrieved from "https://wiki.ch.ic.ac.uk/wiki/index.php?title=It:coursework-2011&oldid=182282"