Installation ------------ Copy the folders "Casts" and "Video originals" from the CD and either the Key.exe or Key.osx for Windows XP or Mac OSX respectively into a single folder on your hard drive. The software will need about 570 Mb. Windows installations sometimes have trouble finding the "Cast" files (with .cst extension), which are all located in the folder called "Casts". On first run it may be necessary to help Windows locate these files manually using the dialogue window that pops up. If you run the application without Quicktime, you will get an error message from the application when you reach a page calling for a movie clip. It is OK to press "continue" at that point. Platform specification ---------------------- This is beta release 0.0 and minimum machine specification has not been established. The software runs on both Windows and Macintosh operating systems, but both require Quicktime (at least Version 7) to be installed in order to see the video clips. Quicktime is free and can be downloaded from http://www.apple.com/quicktime/download/ The following machines have been tested: Windows: Windows XP Pro Quicktime version 7.0.3 or later Windows XP Home Quicktime version 7.0.3 is incompatible but 7.1.3 works Windows 2000 with 264 Kb RAM Quicktime 7.0.3 Macintosh: OSX version 10.4 with 768Mb RAM. Quicktime version 7.1.3 If you try the software on a platform with a different specification, please let me know the outcome. See the section on "known issues" below. Description (to be printed on the sleeve of the distribution CD) ----------- What is it for? Enables the identification of the most commonly found species of ciliated protozoa in aerobic sewage-treatment processes. The prediction of effluent quality based upon the protozoan populations present may be made, but is not implemented in this release. Who is it for? The information and methods provided require no formal previous knowledge and is primarily aimed at those working in sewage-treatment works it should help them to understand what it happening in their treatment plants. Aerobic treatment processes provide a rich source of teaching material for the classroom and the disc will be of value to schools and universities. What are its features? The disc provides:- 1. Identification keys Uniquely, two fully integrated keys for the identification of ciliated protozoa are provided. Initially the illustrated key should be used. This is particularly useful to the new user and follows the classical approach to identification. However, from time to time you may not be able to answer the question posed (for example you may have a damaged or obscured specimen) which makes it difficult to progress using rigid, classical keys. We therefore provide a second character-based key which may help you progress further. You may switch backwards and forwards between the keys as often as you wish. We provide many shortcuts so that more experienced users can progress through the keys at their own speed. 2. Good diagrams. We have provided the best diagrams available from the literature. 3. Video clips and still photomicrographs. A unique collection of video clips is provided which shows the user how the ciliates move and feed since no matter how good the diagrams are they do require experience to imagine how the different species look in real life. In some cases we provide photomicrographs where video clips are unavailable. 4. Data Recording. A note field is provided for users to record observations or comments about a specific page. The notes are held in a file which can be loaded at the start of an observation session or can be started afresh, as preferred. 5. Effluent prediction. Identification of ciliated protozoan populations may be used to predict the quality of effluent emerging from the plant. The ciliates are identified one at a time and their approximate population density is assessed. Once this is done the effluent quality can be predicted from one of 3 summary statistics given at the top of the profile screen. The data are presented as a list of scores for taxa associated with particular effluent qualities. The likely effluent quality is associated with the category achieving the highest score. The first (left-most) set of scores (in 4 categories) are the Curds and Cockburn (1970) index based on simple presence or absence. The second set of scores are a weighted Curds & Cockburn index taking the relative abundance into account. The third measure is the saprobic index (in 5 categories). In later releases these data will be presented in a more user-friendly manner, while the full data will be presented on an associated Academic page. 6. Handbook [to be implemented]. A handbook may be printed from the disc. It provides full instructions on the use of the keys, how to sample. 7. Bibliography. A full bibliography to the literature is provided. Instructions ------------ Start the application by double-clicking on 'Key'. There is always a button at the bottom of the screen containing a question mark; click and hold to display a help box that tells you what the program expects you to do on the current page. Putting the mouse pointer over the an icon changes it from an arrow to a pointing finger (indicating that the system is ready to accept a mouse click) and the icon's name (also purpose) is displayed. The opening screen allows you to enter the specification of your sample. These data are stored and inserted each time the key is started, but can be over-written for each sample. You can open an existing file for your notes, or create a new file, using the buttons on the lower right of the screen. From this screen you can load a previously saved run of the program which will take you back to the point at which you pressed 'save'. The main program can be accessed by 3 main routes: Pictorial key: intended as a tutorial introduction, it asks specific questions in the order of ease of observation, so the first question asks whether the ciliate is attached or not, probably the simplest observation possible. The Shortcut key gives access to the pictorial key part-way through the identification process, assuming that you know to which group of ciliates your unknown belongs. Terms highlighted in blue have associated help and clicking on them will take you to the help page. The questions allow for uncertainty, so that a species that can have either character (e.g. Stentor can be attached or free-swimming) can be found through either route. If you pass you mouse pointer over the diagrams, the species name will appear on the top of the screen. Click the mouse and you will go directly to that species. For debugging purposes, the question you are now looking at is on the top right of the screen and the place you will go when you click the mouse is on the top left. The icons at the bottom of the screen are explained below. Character key: allows character states to be entered directly. If you position your mouse pointer over a character the character question will appear at the top of the screen and, for debugging purposes, the character code appears on the top left. Click on the character and a window pops up with a list of available states, together with 3 buttons, which closes the window and does nothing else, which takes you to a help page for this character, and which deletes any value currently recorded for this identification. When you select an appropriate value, if there are dependent characters they will now appear on the screen (e.g. if you select "attached = yes", then characters relating to stalks and loricas will appear). Taxon list: is simply a list of currently available taxa, intended for those that are familiar with ciliates to select the taxa present in a sample quickly. Initially the list is 4 columns of genera and where there is more than one species found in sewage, a drop-down menu of species names will appear. Icons: appear as appropriate through the program. Placing the mouse over an icon reveals its name over the icon itself and also (part of the debug tools) on the top left. "Step back" moves to the previous position and deletes any choice made on the current screen. "Step forward" (only in the Help system) moves the reading point to the next available page. "Key" switched between the pictorial and character keys: filling in the appropriate data values during the switch. "List" shows the taxa matching the characters thus far entered. "Notes" opens a window and allows the user to add their own notes: during this debugging phase, please use the notes file to record observations and send the file to Dave Roberts (d.roberts@nhm.ac.uk), which also contains other debugging information about the program status at the time the note was completed. "Print" prints a screen-shot of the window to the printer. "Help" provides instruction on what the program expects you to do next. "Academic" give access to formal nomenclatural, bibliographic and ecological information (see below). "Save" records the results you have entered, including the profile and current position in the identification key. "OK" indicates that the species on screen is in the sample and adds it to the profile (see below). "Next Specimen" re-sets the key to the beginning but retains the profile for the current sample: note that the screen is not quite the same as the opening screen, because you can access the accumulating profile from here directly and you can wipe the profile by moving on to a new sample. Finally "Exit" closes the program. Species pages: when you have identified a species, you will end up at a page with a diagram, a video clip or a photograph if one is available and a species and genus description. From here you can access the Academic page (from the icon) which contains details of taxonomic authorities, synonyms, identification notes, comments on the taxonomic position, bibliographic details, including the sources for the diagrams, and ecological comments including saprobity information. If this is the taxon that you have seen in your sample, clicking "OK" will add it to the sample profile. Profile page: collects a list of species identified in the current sample and requires an estimate of relative abundance. This can be entered either by clicking and dragging on the red portion of the slider bar or by typing (after clicking) a value into the box. The values are percentages. This are used to calculate a predicted value for the effluent based on the associative value (Curds & Cockburn method) or the saprobity of the recorded taxa. Note that saprobity values are quite coarse-grained and the data are grouped, so that small differences in abundance values will not affect the outcome. Help pages: are accessed either through the character key or the highlighted terms in the pictorial key. The "Step Forward" icon will take the reader to a related page which may help to clarify the concept being explained. This grouping of pages is context-dependent and will return to the page from which you started. The "Step back" icon will return you to the page from which you entered the help system. Known issues ------------ The software does run slowly in one or two places, where it is assessing character values against species descriptions. The primary places are notified by an on-screen message, which usually takes no more than 2 or 3 seconds. One such place is entering the character key, where the on-screen message seems to disappear too early. On some Windows systems the pictorial key Q047 (shape-choice) seems to run very slowly. If you observe this, please let me know the details of your machine configuration (mail to dmr@nomencurstor.org). If you run into this problem, please be patient with this release and wait for the cursor to look like a pointing finger before clicking. If you outrun the program you will confuse it and results are unpredictable. The state parameters (name of works etc.) are stored in a preferences file called Key.txt on the Mac and located under Macromedia Preferences with the application itself. I can't find the same file on Windows machines, but it must exist. If someone can give a clue to the location, I'd be grateful. Reporting problems ------------------ The 'Notes' facility has been implemented and, for this early Beta trial, records various state parameters, including the path to reach the page in the file, invisible to the user. The user can add visible text which will be recalled if a note is added to the same page later. Please use the notes pages to record problems, comments or matters requiring attention for the page concerned, the e-mail the file to me. Please remember that the notes are note kept in order, so phrases like "as in the last screen" are not helpful. On this disk is a FileMaker database that can be used to read the notes file (by importing) and makes understanding what's there a bit easier. The FileMaker db accepts the notes as a single string into each record and then uses macros to dismantle the string into its component parts. An alternative method is to save the program at the problem point and send the file with an e-mail explaining the problem. New to this release -------------------- The save and restore features are new to this release. They use '.wwk' as the file extension, but are simple text files. Similarly the Notes files use an ".asc" extension and are also simple text files.