Difference between revisions of "UserGuide:Neuron Search"
(New page: This search page is (we hope) designed to be largely self-explanatory. There are some points about this page that may not be obvious, though: http://www.wormbase.org/wiki/images/I_neuron1...)
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Latest revision as of 18:30, 17 August 2010
This search page is (we hope) designed to be largely self-explanatory. There are some points about this page that may not be obvious, though:
"Selected a Class": Not all classes are intuitively reasonable. For instance, 'head neurons' only includes four neurons and not (e.g.) amphid neurons! The safest rule to follow is that if a set seems not to have the neuron you want, you should scan that set with no filter (or with "*" as a filter) to see if (for whatever reason) the neuron is simply not considered a member of that class. "Set a Filter":
This allows a class of neurons to be selected for only those neurons with a certain text string in their names. The "*" formalism for 'zero or more undefined characters' (from UNIX) is used; for example, searching for "BDU*" in the "neuron" class will give BDUL and BDUR. Another UNIX metacharacter that is used is "?", to denote 'exactly one undefined character, not zero or more than one'. "Submit a Search Job":
You need to click the "Find" button to start a search for neurons in a given class and with given filters.
You must click on one or more cells given in the list to specify which you will have displayed in detail. To get two or more cells, you must (somewhat confusingly) hold down the "shift" key on your keyboard while clicking on the second or later cells (otherwise, each time you click on a cell, all the previous cells you have marked by clicking on them will be un-marked). "Add Selected Neurons to the Field Below":
After you have selected one or more neurons in the "List", you can click on "Add Selected" to get these listed as neurons to be displayed. Alternatively, you can click on "Add All" and get all the listed neurons tallied at once for later display. "Selected Neurons for Display":
If you have followed the procedures above, you should have one or more neurons listed in all-capital text, separated by individual spaces, in the empty field to the right of this step.
NOTE! One shortcut that is not mentioned but can be quite helpful: you can simply type in by hand one or more neurons into the empty box next to "Selected Neurons...". If you know exactly what neuron you want, this can save considerable clicking and so forth. It can also let you construct a list of neurons that fit your specifications rather than any list that Wormbase has precompiled (e.g., "all the neurons that express tax-2", a set that includes both amphid and non-amphid sensory neurons, and is difficult to define by predefined sets but easy to type in). Also note that this is not forgiving of typographical errors or incomplete names: if you type "BDU", the Wormbase server will not know that you mean "BDUL or BDUR or both". "Display Data for Selected Neurons":
This gives two different options. You can ask for "Summary Data" or "Wiring Data" by clicking on the correct button. "For Summary Data, Select One or More Properties and Click Go Button":
This field appears after you click on the "View Summary Data" button. It gives you the choice of what fields of information you would like to display. The default ("Select All Fields") will show everything defined as "Summary Data"; other choices are more restricted. It is probably most useful to set restricted choices when there are many neurons to be compared.
Clicking on the "Go!" button will then (finally) generate a table with the requested data fields.
"For Detailed Wiring Data, Check Radio Buttons and Click Go Button":
This gives choices of connection type, strength of evidence for connections, and the specific animal from which connections were ascertained. Again, clicking "Go!" generates the full data display.