Laboratory ObjectivesDuring the lab time allocated for the IT course (six sessions in total in the autumn with two in each of weeks 2,3 for all students, and two sessions in either week 4 (Group B) or week 8 (Group A), you will be expected to achieve the following objectives:
The Computer lab is formally booked for CIT work during weeks 2-3 for everyone and then weeks 4 or 6 for specific groups(see times). CIT students have absolute priority during these period. 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. You also 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.
- To gain experience in the use of specific programs such as
- Word (either the Microsoft version or an Open version) in combination with the EndNote bibliographic database
- Several different chemical structure drawing programs
- Remote window network based programs
- World-Wide Web browsers and Wikis
- Programs specific to chemical information searching
- To learn how to cope with "bugs". You will encounter (unfortunately) several in this lab, and we have suggested "workarounds". [Bugs and other oddities are explained in square brackets where we know about them. If you discover your own, please let us know].
- To experience several different ways in which chemically specific information can be searched for, ranging from simple keyword searches to 3D structure searches
- To gain experience of different data formats used for expressing chemical information, and how to interconvert them, and use them in populating Wiki pages
- To apply the above skills to doing a comprehensive literature search on the molecule Penicillin, a reaction (its conversion to Cephalosporin), its properties, both physical (spectroscopic) and biological, and how to create e.g a Word document organising these themes.
- You will then have to perform similar searches on a project molecule chosen from a list on the Wiki, the outcome in this case being a contribution to a Wiki article.
The lectures contain 28 bullet points which we feel you should be familiar with. The number indicated against each lab activity relates to each numbered item.
The first session in the first week is reserved for computer familiarity exercises. Start by checking that your login still works.Next, you will use some chemistry specific programs you might not have come across in first year. There will be demonstrators available to show you how to do this and answer your questions. Do please ask them if you dont know what to do next, or are just confused by it all! And remember: Computers crash and do odd things. IT, at least in part, is the process of learning to cope!
If you complete the above, do feel free to move on to the coursework below.
Log-in 1. Perhaps the single most confusing aspect for most people is what the Home icon (right) means. So let's sort this out immediately. On the computer desktop, this icon means "a 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! [The next generation of Windows may weaken or lose this metaphor, so be warned!]. 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. [This connection between Home and "My Documents" is not always true, but is set to be true in the chemistry department].
Start FireFox using the icon on the desktop. [Why not Internet Explorer (IE)? Well, it handles some of the chemical stuff more delicately than Firefox, but it mostly works, so if you are really keen on IE, go ahead and use it]. You will discover another "home" (right) . This means "the Web page designated as the starting point for Web navigation in the College/Department".Open the Web URL http://teaching.ch.ic.ac.uk/it/ (it should be listed in the Bookmarks menu and in the tabbed menu along the top of the browser window). [Of course, this instruction might strike you as pointless, since if you are reading this, you will have already opened up a browser at this page!]. 6
Start Microsoft Office 2007. The basic (Home) Word document work area is shown to the left 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. In particular, open/save/print dialogs are now to be found by pressing on the Icon highlighted here with a red circle. Copy/past operaations are invoked using the icon encircled in purple. Other common operations are found to the right of these two, 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.
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; 1. Go to Programs/Additional Programs/EndNote/Configure EndNote. 2. 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"].
Images are special when it comes to copying. Proceed as follows:
- 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:
- If one of the options is Copy this 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).
- 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.
- 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.
- Not everything is always "copyable". Some apparent images are in fact produced by a "plugin" or "applet" embedded in the browser. This includes most conspicuously chemical diagrams, such as may be found on these course notes. Here a copy or a save operation will in fact save e.g. molecular coordinates (i.e. "data") rather than an actual image. To regenerate any image from such coordinates, you would have to import them into a suitable molecular modelling program. Try "right clicking" on the rotating DNA molecule on the start page of this documentation to see if you can rescue its coordinates!
- Practice naming and saving document files to (a) local hard disk, (b) a network storage area such as Home (Drive H: on Windows) or Mac-PC (a temporary exchange area for Macs and Windows) (c) a removable medium such as a PenDrive or (d) a writeable CD or DVD. You have to provide your own blanks for the latter. [Not every machine has a CD/DVD Writer. If it does not work, you have found one of these machines!].
- Practice finding files 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!] 3
Starting and using ChemDraw. If you click on the Chemdraw icon in the toolbar of these notes at the top (second along) you will start Chemdraw as a separate program. Practice by drawing Penicillin, drawing what you see below.
When you are happy with your own drawing of Penicillin, try reproducing that of Taxol (right hand diagram). 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. Then repeat the procedure by clicking on the image of Penicillin or Taxol above to get a "one I did earlier" copy (it should give you C47H51NO14. Mol. Weight 853.91). Do you get the same values as the pre-recorded one? 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?4
- Checking that a simple Java-based program works, and using it to calculate a molecular mass. Why is this different from a molecular weight? 5
- Practice creating a .zip Archive of two or more files using WinZip (Windows). Windows users will have to open WinZip.exe from the Start/Program files menu, create a new archive, and drag-n-drop items into it and then save to create the archive.3
- Setting up E-mail, sending a document as an attachment (to yourself) and good e-mail housekeeping and etiquette. Create an archive of files (see above), and email it to yourself or a friend, and check you can unpack and read the archive. 3,5
Digital Certificates. This is a mechanism whereby an email or a Word document (also Acrobat) can be digitally signed to ensure it has not changed since signed, that it truly comes from the signer, and has a clear time stamp associated with it. A Imperial College digital certificate is automatically issued to you when you log in.
- To send a signed (i.e. trusted) email, open up Outlook 2007 and from Tools/Trust Centre/E-mail security check the Add digital signature to outgoing messages button. You need only do this once, and all subsequent emails will be signed. Whilst you are in this panel, also click on Settings, and from there Choose a Signing Certificate. Only one should be on offer. Select it, and close the Change security settings box. Now click on Publish to GAL. This publishes your certificate so that others can find it (they would need your certificate if they wish to send you an encrypted (as opposed to signed) email. It make take up to 30 minutes for your email to become searchable. When you compose a new message, a Sign button will appear in the taskbar (red circle, left) which you can select/deselect as appropriate.
- An alternative to using Outlook is the Web interface (using Internet Explorer and URL: https://icex.imperial.ac.uk/Exchange/ ). Go to Options and thence E-Mail Security. You will be asked to download an S/MIME control. If you are using your own machine, you can install this. Currently, this installation is not possible on College machines (but watch this space).
- To sign a word document, create it, then from The top left icon, Prepare/Add a digital Signature. Close the panels and save the document. You need to do this for each document you wish to sign.
- Yo can combine the two operations, i.e. sign a document and then sign the email you use to send it to someone. You may be asked to use this combination when submitting course work to laboratory supervisors.
- Search for other people's certificates here. If you have in your possesion your own certificate and another person's certificate (the public key thereof) you can go one step further than signing, and proceed to encrypting either the email, or the document, or both. Only you and the person whose certificate you have included will be able to read the resulting email/document.