| |
List
of Figures
Figure 1 : Information Space
Figure 2 : WCS Search Window
Figure 3 : Document Display with Figures
Figure 4 : Display of Forms (Biological Data)
Figure 5 : Display of Cell Lineage
Figure 6 : Display of Physical Map
Figure 7 : Set of Results
Figure 8 : Simple Search Window
Figure 9 : Full Search Window--Two methods of searching
Figure 10 :Browser and Type Selection Menu
Figure 11 :Browser and Locator box
Figure 12 :Subsearch
Figure 13 :Panel--Type & Field Restriction menus
Figure 14 :Panel--Parentheses, Boolean Strategies, Shortcuts
Figure 15 :Thesaurus
|
Figure 16 :History menu
Figure 17 :Links, Show and Follow
Figure 18 :Links, from a set
Figure 19 :Utilities menu, quit
Figure 20 :Do the Gripe Thing
Figure 21 :Login Window & New Person Object
Figure 22 :Entering new data
Figure 23 :Pasting objects
Figure 24 :Annotating Data
Figure 25 :Editing Data
Figure 26 :Start a link
Figure 27 :Finish a link
Figure 28 :Permissions window
Figure 29 :Setting Permission
|
Acknowledgements
Community Systems Laboratory (CSL) is affiliated with the Graduate
School of Library and Information Science and the National Center
for Supercomputing Applications at the University of Illinois, Urbana-Champaign.
This research was partially funded by the National Science Foundation
under grants IRI-90-15407, IRI- 92-57252, and BIR-93-19844. Additional
support was provided by the University of Arizona and the University
of Illinois.
In addition, the National Library of Medicine provided a copy of
the IRX search software, which was then modified and adapted for
the Worm Community System (WCS). Terry Friedman wrote much of the
original "back end" of the system. John Calley developed
the lineage display. Hsinchun Chen created the Thesaurus functions.
Thanks to Jean Thierry-Mieg and Richard Durbin for the genome data
from ACeDB. Theresa Stiernagle and Bob Herman provided stock data
and edit the Worm Breeder's Gazette (WBG). In earlier days of this
project, this data and much additional help was provided by the
former curator of the stock center, Mark Edgley. Finally, we are
grateful for the many comments from the users of WCS, the worm community
itself.
The user manual is a collaborative effort by members of the Community
Systems Laboratory team: Albert Cheng, Ed Grossman, Curt Jamison,
Brad Mills, Kevin Powell, Beverly Rauchfuss, Bruce Schatz, and Laura
Shoman. Final editing and text preparation was done by Laura Shoman.
The HTML version of the user manual was created in part using the
macintosh program rtftohtml2.0, available wherever NCSA Mosaic is
found.
(c) 1994 by Community Systems Laboratory, University of Illinois,
all rights reserved.
All brand names or product names are trademarks or registered trademarks
of their respective companies.
Quick Start Worm
Community System
Finding Things
To search for a term, enter the term in the simple search window
(see Figure 1), and press the return key. The results of your
search  appear
in a new window. If you want to perform a more sophisticated search,
click on the Full Search Window button (see Figure 2). Click on
the Query Specification box under Search All (to move the cursor
into That box). Type your search term. Limit your search to
a particular data type by selecting the type of data you want
to search using the Type Selection menu; then click on Search
This Type. To perform a complicated search, restrict the type
of data searched, fields within the data types, and add additional
terms by using the Panel functions. Panels also employ AND/OR
searching. To locate a known object to view, select the type of
data you want to examine by clicking and holding on the Type Selection
menu under Search This Type; highlight the type of data you wish
to search. Type words in the Locator box. Objects automatically
scroll through the Browser window. Completely type your word(s)
and Return OR click on the object as it appears in the Browser
window. The object is retrieved in a new window. To identify Related
Terms, use the Thesaurus. Enter a query in the Query Specification
box; then click on Thesaurus to see other terms that occur in
relation to the term you've selected. A search from the Thesaurus
window will automatically search all types. To view the cell lineage,
click the Lineage button on the simple search window, or select
cells from the Type Selection menu and type your cell name in
the locator box.
Viewing Results
The result of a search is displayed as a set, a list of objects
of various data types. Point to an item in the list and double-click
on the item to retrieve it. Retrieved objects are displayed in
a form, document, lineage, image, or a set, depending on the type
of data you located. Objects within WCS are linked. For example,
you can move from gene to document to clone to the physical map
by traversing the links between them. Most fields and italicized-and-underlined
terms within each display are objects that are linked to other
kinds of data or displays. Double-clicking on an object will retrieve
that object.
Navigating the Information Space
Once you retrieve results, use the Links menu on each display
to navigate the space. Show Links from an object or selected field(s)
within the object will display a list of the objects linked, which
you can then double-click on to traverse the link to a new object.
Follow Links from the object or selected field(s) within the object
to all related objects. From the Utilities menu on any Results
window, you can return to the Search Window. From the Search Window,
you can review the History of the windows you have opened, and
scroll down the list to return to a previously opened window.
Quit from the Utilities menu on the Search Window.
Overview
The Worm Community System (WCS) is a digital library developed
by Community Systems Laboratory (CSL), now located at the University
of Illinois, Urbana-Champaign. This digital library contains information
about Caenorhabditis elegans and a software environment that
enables you to interact with this community library across the international
computer network, the Internet. The functions of the software environment
enable you to (1) search and browse the existing knowledge of the
community and (2) add your own data and literature to the library,
for your own private use, collaboration with colleagues at local
or remote sites, or for wider distribution to the community. The
purpose of the system is to support the display and recording of
patterns in the information space, where the patterns are formed
by links between objects and represent important relationships.
The capacity for dynamically updating the information, both from
central archives and from local labs, should help to better propagate
the knowledge across the community.
WCS Contents
The information in the worm community library attempts to span
the range of all that C. elegans researcher might find useful,
including formal and informal literature and data. The literature
includes some full text articles and abstracts from most of the
CGC bibliography (current to 2017), full text of all articles from
the complete Worm Breeder's Gazette (WBG), and citations
from the most recent worm meetings. The data include genomic data
from the MRC/WUSTL mapping and sequencing project (genes, maps,
sequences), community data from the Minnesota stock center (strains,
people), and the beginnings of cellular data (cells, lineage).
As a tool, WCS complements ACeDB. WCSr2 contains version 2.14 data
from ACeDB. Although WCS and ACeDB are both hypermedia-based biological
databases, they differ in a number of ways. WCS is a community system.
To that end, it allows interactive creation and editing of new objects
by end-users within the system. WCS also supports editorial and
privacy controls, allowing users to restrict access to data and
to determine how reliable a particular piece of data is. Finally,
while ACeDB distributes its database with the software, WCS has
a client-server architecture with a central database. This allows
all users immediate access to new data, instead of relying on periodic
updates of the database. This feature supports the collaboratory/community
system goals of WCS.
What's New in r2.0
--As mentioned above, the system architecture in this release is
different from that in WCSr1. Release 2 has a client-server architecture
with a central database. This allows for instantaneous updates from
both the central site (CSL), and the remote labs connected to the
system.
--There is no gateway to the ACeDB database from the WCSr2 interface.
--New functionality to facilitate publishing of new
data. See page .
--You can enter new information of any known type
as documents or forms. See page .
--You can restrict access to data you enter to control
its propagation to the community. See page .
--Two types of search windows are available: a quick, simple search
window and the Full Search Window that allows several different
methods of searching . You can search all the data, or restrict
searching to particular data types and/or fields. You can also create
complex searches using Boolean operators (AND/OR). See pages 12,
and .
--You can browse different data types, selecting a
specific name within a type to gain direct access to related information.
See page 12.
--You can revise your personal information (lab affiliation,
phone number, address, etc.). See page .
--Lab directors (those listed as Lab Representative in the Lab objects)
may revise laboratory information . See page .
WCSr2 is under continued development. As a research prototype, portions
of the interface, levels of functionality, and data are subject
to change. While this manual attempts to cover many of the features
of the system, changes are ongoing.
The most current documentation will be available at the anonymous
ftp site, csl.ncsa.uiuc.edu. We appreciate your patience, and we
welcome your comments and feedback.
Where WCS Runs
Although you run front end software from the computer in your local
laboratory, you are accessing data located on a server at the University
of Illinois, Urbana-Champaign. All of the data for the system and
much of the application is stored there, while the front end, the
"window management" and other aspects of the application,
are loaded on your local Sun workstation. The information you access
from WCS comes across the Internet. The knowledge that you add to
WCS is automatically propagated to the community, or to a group
you select. The software environment provides for transparency,
providing a simple uniform set of commands for the library of community
knowledge, and hiding from the user the complexities of handling
the different physical locations and the different data types.
If you have comments or suggestions
Community Systems Laboratory has moved from the University of
Arizona to the Graduate School of Library and Information Science
and the National Center for Supercomputing Applications at the
University of Illinois, Urbana-Champaign. Your comments, questions
or suggestions are always welcome. Please email them to wcs@csl.ncsa.uiuc.edu.
You can also send a Gripe from within WCS. The gripe function
is on the Utilities menu on the Full Search Window.
If you need additional help
If after reading this manual you need additional assistance in
using the application, you can contact the Community Systems Laboratory
through the email address, wcs@csl.ncsa.uiuc.edu.
Where to get WCS Software and additional Documentation
The front-end needed to run WCS is available via anonymous ftp
from csl.ncsa.uiuc.edu (141.142.221.11). The instructions
and other configuration information are available in Appendix
1: Getting and Installing WCS. This users' manual is also
available via anonymous ftp from csl.ncsa.uiuc.edu. Formats include
Postscript, and plain ASCII Text. You can also request a printed
users' manual by writing to us at wcs@csl.ncsa.uiuc.edu.
Please review the Systems Requirements below.
Announcements of WCS data and feature updates will be announced
in the Worm Breeder's Gazette, on the usenet group, bionet.celegans,
and on the celegans mailing list. See Appendix 2 (page ) for additional
information about these and other Internet resources of the C.
elegans community.
This manual assumes that you have already installed and configured
the Worm Community System software in your lab, and that you know
how to perform each of the following tasks within a graphical
user interface using a mouse:
--Click on an object to select it;
--Double-click on an object to perform some related function;
--Shift-click to select multiple objects;
--Drag, to re-size a window, move a window, interact with pull-down
or pop-up menus, or select multiple contiguous objects;
--Choose a command from a pull-down or pop-up menu;
--Choose options (radio buttons, pop-up menu items);
--Interact with dialog boxes;
--Scroll windows using scroll bar and arrows.
If you don't know how to do these tasks, please consult your computer's
users' manual.
Words of special interest appear in bolded italic type.
System Requirements
Network Connections
You will need to have an Internet connection from a Sun workstation
(the local client) in order to access the CSL server. (The data,
search engines, thesaurus server, etc., reside on the Community
Systems Laboratory (CSL) server at UIUC.) If you choose to run a
node off the local Sun workstation, you will need an Ethernet connection
between the workstation and the node.
Local Client
We suggest the following machines for local clients: SparcStation
5 (a fast, good machine), SparcStation LX (older, slower, but less
expensive), SparcStation 10 or 20. The system can also be run on
slower, less expensive machines such as the SparcStation 2, 1+,
and IPX. The Sun station should run at least 32 megabytes of RAM
(more is better, 64 or more is optimal).[1] These workstations should run version 4.1.x of Sun's operating
system. We strongly suggest that you run SunOS 4.1.3U1. Alternatively,
you can run Solaris 2.3 or later. We have not tested WCSr2 on earlier
version of Solaris. You must have the SunOS 4.*.* binary compatibility
package installed to use WCSr2 with Solaris. To determine your
current OS, type uname -a at your Unix prompt.
X-Windows Environment
The local software (front end) requires an X-windows environment
and, in addition to that environment, will take approximately 10
megabytes on a hard drive. This disk space requirement may increase
over releases, but no dramatic increase is anticipated. On Sun workstations,
we use both X11R5 and OpenWindows (the Sun product) with good results.
You should run OpenWindows 3.0 or later, or X11R5 or X11R6. We run
MacX on our Macintosh node. The previous release ran fine on a PC-clone
using the NCD X- windows package. If you need help in determining
what X-windows environment you currently use, see Appendix 3, Troubleshooting,
at page . Our recommendation for operating system and window
system: Optimal: SunOS 4.1.3U1 with X11R5; Absolute minimum:
SunOS 4.1.1 with OpenWindows 3.0.
Nodes from your Local Client
If you run a Macintosh node, your Mac should have a minimum of
8 megs of RAM (more is better, 12+). The Mac should also be in the
68040 processor family (faster is better). Higher-end 68030 Macs
will run MacX acceptably IF no other applications are running. If
you run a DOS-based node, your node should have a minimum of 8 megs
of RAM (more is better). The processor should be a 486/66 (faster
is better).
The node monitor should have a resolution of 1024 x 768 pixels.
Apple's 16" monitor has a resolution of 800 x 600 pixels and
has been called tolerable by some of our users here. One site is
using an NEC MultiSync 5FGe Monitor on a Mac Quadra 650. NEC has
control panel software ("DPI on the fly") that allows
for changing the resolution of the monitor on the fly while the
machine is running (no rebooting): thus, one can change between
1024x768 for WCS, and return to 832x624 or 640x480 for word processing.
See Appendix 2, page .
Input Devices
The graphical user interface requires a keyboard and a mouse (or
trackball) input device.
Output Devices
Printing can be done from a Sun workstation transparently using
a shell script available from CSL (see page ); Printing from a Macintosh
is done through MacX.
--Also review Appendix 1: Getting and Installing WCSr2, page .
Concepts
Information Space
You can think of all the knowledge in the library as existing in
an information space. All the knowledge in the system consists of
objects, also called information units (iu or ius (plural)) which
are interconnected via relationship links to form the space. The
information space is much like a web. The information units are
points within the web. Links are the threads of the web, giving
definition to the space while being a part of the web itself. Figure
is a very simple representation of the information space.Click
here for Picture
Types
Object types (sometimes referred to as data types) include 2 and
3 factor data, deficiencies, genetic rearrangements (e.g., translocations),
strain names, gene names, chromosomes, contigs, clones, sequences,
cells (lineage history), documents, images, persons and labs. (In
ACeDB, these are referred to as Classes.) You may enter new data
that is recognized by the system as one of these types.
Navigating the Information Space
You view the space of existing objects by first issuing a search
to retrieve objects and then navigating links from these objects
to other related objects. You can also share your own objects with
the community by adding them to the space. You first issue a command
to create objects and then make links from these objects to existing
related objects. Commands can be issued upon a selected object,
thereby manipulating the information. The basic commands are the
same for all objects in the system. Once you have learned the basic
commands, you can use them on any object or collection of objects
(a set). Commands are issued by clicking on command buttons and
by selecting items from pop-up menus that are available in various
windows (see Figure 2, and below).
Interface Conventions
The Worm Community System utilizes a graphical user interface.
The full Search Window is the gateway to WCS. See Figure , below.
The display on your local monitor may vary from the display used
in this manual, due to equipment differences. However, the general
principles discussed here apply to all kinds of displays. Click
here for Picture
Unlike other windows within WCS, you may not resize the Search
Window. And, you may not close the Search Window. To Quit the program,
select Quit from the Utilities menu on the Search Window. To go
to the simple Search Window, Figure on page , the small window that
first appears when you start up WCS, use the Utilities menu option.
The two search windows may not be open at the same time.
The Search Window contains elements common throughout the rest
of the application: pop-up menus, boxes, objects, buttons, and scroll
windows. In order to perform a function, e.g., issue a command to
an object or enter data into a field, the object, box or field must
be selected. A selected item will be highlighted in some way, either
by a rectangular outline, or by a reverse highlight (white characters
on black background). In the case of a box or a field, the cursor
must be in that space before data can be entered. You can type into
a boxed field as well. Depending on the function being performed,
data may be entered by (1) typing characters; (2) copy and paste
functions; (3) selecting data from pop-up menus; or (4) toggling
between choices.
Pop-up menus in the Search Window include the Type Selection menu,
and the Type and Field Restriction menus. You can type queries or
names of known objects in the Query Specification box and the Locator
box. Buttons in windows indicate Tools, Commands, or pop-up Menus
that list options. Tool buttons are New and Thesaurus; Command buttons
include Search All, Search this Type; Menu buttons are Panel, History,
and Utilities. Scroll bars (on the right side of the Browser Window,
for example), allow movement through each window. As information
is added to a window, scroll bars may appear on the right side,
or on the bottom (to permit scrolling left and right across an image
or lineage).
Displays of Types
The displays include documents for the text types
(literature abstracts, newsletter articles, meeting abstracts and
citations, etc) and forms for the biology object types
(genes, clones, etc.).
Documents are displayed as scrollable windows of formatted text.
Documents may have images associated with them (figures, tables,
or line drawings--see Figure ). To retrieve any existing images
, display the document. The Display menu item, Show Images, will
be enabled if figures accompany the selected article. Images may
also be retrieved as objects of a set, or by showing or following
links from a documents.Click here for Picture
Forms of biological data are displayed as scrollable windows of
fields with names and values (see Figure ). Click
here for Picture
Some types have a dynamic, graphic pictorial display. For example,
cells are displayed as lineage (Figure ), allowing a user to view
information on a particular cell, and then interact with the
data , following development of the cells through generations,
linking cells to other objects within the system, and viewing images
of the anatomy. Click here for Picture
A set of clones is displayed as a region (or regions) of the physical
map (see Figure ). If the set of clones was generated by a series
of searches and navigations, the pictorial display provides a method
for determining how they are clustered across map regions. Graphic
displays have the same dynamic functionality as other displays so
that you can select individual objects and follow or make links
to them. Click here for Picture
Sets
A set is a collection of objects that can be operated on as though
it were a single object. The results of a search form a set
of related objects. The links on the entire set (or any
subset) can be followed with a single command, e.g. find all of
the genes linked to all the articles mentioning sensory and perception.
The links to clone objects from all of these genes can then be followed
to locate all the map regions containing these genes. The display
of a set is a list of all the items, displayed via a one-line summary
for each (see Figure ). Click here for Picture
Links and Embedded Objects
The displays of documents, forms, graphics, and sets are themselves
composed of other objects referenced within the display contents.
These referenced objects can be selected and displayed.
For example, a gene name occurring within the text of a document
is a "live" reference to the corresponding gene object,
which can be retrieved by double-clicking on the gene name. In the
document in Figure , the term unc-5 is an object that
is embedded in the text. Double-clicking on the object traverses
a link, an active connection between the gene name within the document
and the corresponding gene form object.
Similarly, a clone name occurring within a field of a form is a
"live" reference to the corresponding clone object, which
can be retrieved by double-clicking on the clone name. Double-clicking
on the field Clones in the object gene: mec-7 would retrieve the
object for clone:NW#B4 (see Figure , above). The link, as an active
connection, records some relationship between the objects (e.g.,
document and gene, form and clone). The objects can be selected
and their links can be followed.
See the sections below on links at pages and .
Searching Data
There are two methods used to search the system: querying and browsing.
The simple search window that appears when the system is started
contains a simple query window. Click here
for Picture
Type a term in the box and press the enter key to search all of
the data within the system for your term. After you enter your term,
you can use the Thesaurus to review terms associated with your term.
You can also gain easy access to the cell lineage display.
The Full Search Window accommodates both browsing and querying
(see Figure ). You can mentally divide the window into two parts:
the Browser tool (on the left), and the query specification functions
(on the right). The Browser is also used when adding your own data.
Click here for Picture
Browser
The Browser is a way to locate known information by type
(allele, chromosome, gene, contig, person, etc.). The Browser
consists of the Type Selection menu, the Locator box, and the Browser
window. Click here for Picture
To use the Browser, select the type of data you wish to browse
using the Type Selection menu (on the left side of the Search Window.
See Figure ). The selected type appears in the Type Selection menu
and the list of objects related to that type appear in the Browser
window.
In our example in Figure , gene is the object type that has been
selected. The Browser Window contains the names of all gene objects
in Figure . Click here for Picture
If you know the name of the object you want to view
, you may begin to type it in the Locator box, to the right of the
Type Selection menu. (Be sure the cursor is sitting in the Locator
box before you type. If it is not, click on the Locator box and
the cursor will appear. If there is data already in the Locator
box, you may drag across the data to highlight it, and begin typing
your new data.)
In our example (See Figure ), we have typed in the letters m-e-,
and the names in the Browser window have advanced to items beginning
with the letter, m. To view an object whose name appears in the
Browser window, click on the name. The object will then appear in
a separate window. You can also type the complete name of the object
in the Locator box and then press the Return key. The object will
then appear in a separate window.
To view the cell lineage, click the Lineage button on the simple
search window, or select cells from the Type Selection menu and
type your cell name in the locator box.
Query Specification
The broadest search of the data is performed when you type a word
in the Query Specification box and then click on the Search All
button (See Figure ). The application first stems the word you entered,
removing suffixes, and then looks for the matching characters in
the documents and forms. If you enter a phrase in the Query
Specification box, the application does not look for the phrase,
but for the stems of each word, presuming an "AND" between
them.
The results of your search are returned in a new window as a set
of results. If no matches exist, a dialog box will inform you.
Subsearch
If you perform an initial search and you think the results are
too numerous, perform a subsearch. The subsearch will search
only those objects retrieved in the initial search. In our
example, we retrieved 50 items pertaining to mec-7. In our subsearch,
we have used the same term, mec-7, but we have restricted the type
of objects that will be searched to documents, and we will only
search the title field within documents (See Figure ).
Click on the Subsearch button in the Results window to search only
the result set (50 items in our example) for the term or type/field
we have stated in our subsearch query. Our subsearch produced nine
documents that have mec-7 in the title.Click
here for Picture
Limiting Searches
Restricting the type of data to be searched, as we did in the subsearch
above, allows you to focus on a specific source, be it a document
from a particular journal, a certain allele, or a particular author.
The Type Restriction menu and Field Restriction menu found in the
Panel provide this flexibility. There are two ways to restrict your
query to a particular type of data.Click here
for Picture
One way to search only one type of data: select the
type from the Type Selection menu (on the left side of the Search
Window, underneath Search This Type). Click on the Query Specification
box and enter your query. Click on Search This Type. The application
will search for your query and return only objects of the type you've
selected.
You can also perform the same search by using the Panel's Type
Restriction menu (see Figure ). Type your query in the Query Specification
box. Use the Type Restriction menu to select the type(s) of data
you want to search. Click on Search All. In this case, your search
will be restricted to the type you've specified. The Type Restriction
menu provides the option of adding or removing types from the Type
Restriction list.
Panel
We've looked at a few ways to customize searches, using the Browser
features and subsearching. We used the limiting example to touch
on a very powerful search tool in WCS: the panels.
Panel refers to two things. First, it refers to the button that
appears on the Full Search Window. This button is a menu that allows
you to add panels, remove panels, and use parentheses in your search
statements. A Panel is also that part of the Full Search Window
made up of the Query Specification Box, the Type and Field Restrictions
menus, and the Boolean box that appears after a second panel is
added to the Full Search Window (see Figure and Figure ).
As you may have guessed, you can use a Panel to "stack"
your query terms and customize your search strategies. For example,
a review of the set retrieved for mec-7 (seen in Figure , above),
indicates there is some relationship between mec-3 and mec-7. There
are also references in the titles of the articles to touch neurons.
Instead of searching for mec-3 and then for objects related to touch
neurons, using Panels will allow searching for all three objects
and their related objects, and will return the results as one set.
We can then continue to navigate this one set of data, instead of
moving back and forth between three sets. Click here for Picture
To add a panel, choose Add Panel from the Panel menu. As you can
see from Figure , you can also remove panels. Employing the Panel
function enables you to use Boolean logic in your query. Two or
more terms can be combined in one search using AND and OR as part
of your query.
In our example, we'll use the short-cut of the Type
Selection menu to specify documents as the data type to search (see
Figure ). Since we want to gather information about touch neurons
in relation to mec-7 or mec-3, the Boolean box that appears next
to the Panel button is toggled to OR after the first panel. Our
Search Query becomes "(mec-7 OR mec-3) and touch neurons"
in Documents. The search is done by clicking on the Search This
Type button.
Complex and powerful queries are manageable using multiple Panels
and incorporating parenthetical Boolean statements within a search
query. Complex searches may involve one or more terms being searched
for in more than one type or field within a type.
Thesaurus.
Click here for Picture
A helpful tool in searching is the Thesaurus, a tool that provides
a list of terms associated with the term(s) specified in the Query
Specification box. Clicking on the Thesaurus button opens the Thesaurus
window (see Figure ). The Result Terms are not synonyms or semantically
related terms for the Query Terms, but rather, terms that appear
within the Information Space in association with the Query Terms.
The Thesaurus reflects frequency of term co-occurrence within
the system. In our example, the term microtubules occurs
at a greater frequency with our Query Terms than differentiation
or cell. Searches can be done directly from the Thesaurus, providing
a flexible alternative to the Search Window. Result terms can be
added to the Query Terms by selecting the chosen Result Term and
clicking Add to Query. Alternatively, terms previously used in the
query can be removed. Select the Query Terms to be removed and click
Remove From Query. Remove All will remove all query terms. A fresh
query can be started using a New Query Term. Click the Search button
to begin a query from the Thesaurus. The search performed
from the Thesaurus Window is performed within all data types
, not on those types that may have been specified in the previous
query.
History Menu
After viewing a number of windows, you may want to re-trace your
steps to earlier windows, or you may want to pick out one window
to review. The History menu, located on the Full Search Window,
allows you to review the windows you have opened. Select an item
from the History menu to retrieve it. Click
here for Picture
Links Menu
Once you have retrieved a set of objects as a result of your search,
use the Links menu on each display to navigate the information space.
Show Links from an object or selected field(s) within
the object to display a list of the objects linked. You can double-click
on the objects in the list to traverse the link to the new object.
Follow links from the object or selected fields to
display the linked objects themselves. In the example in Figure
, the search for mec-7 retrieved 52 objects. One is of particular
interest: allele e1506. We retrieved the object (double-click).
We'd like to see a list of the objects linked to it (show links)
and after reviewing the list, we'd like to see each object ( follow
links). Click here for Picture
Another way to view links to particular objects retrieved in a
set is to use the shortcut shown in Figure . In a set, objects are
listed one per line. When an object has links, you can quickly show
or follow links by clicking on the star in the left margin, which
will pop up a "mini Link menu" -- Show Links or Follow
Links. Click here for Picture
Display Menu
The Display menu appears on sets and individual objects, as seen
in various figures above. Display has a menu of consistent options,
but the availability of each option is dependent on the context
of the menu display. For example, if a document has associated
figures , the Display menu option, Show Images will be made
available. Likewise, Copy, Cut, Paste, Delete, Open Selected, etc.,
will only be made available as your login status and ownership status
allow. If you are not the owner of an object (see the section on
Adding Data, page ), you will not be able to delete an object or
any fields within the object. If you have not selected an object,
you may not open it. If you have not logged in, you may not copy
or paste an object (embedding the object in a new object).
Utilities Menu
Click here for Picture
The Utilities menu will appear on many different windows throughout
WCS. The items found in the menu are dependent on the context of
the menu. For example, the Search Window has a Utilities menu (see
Figure ) that includes options to gripe to the programmers at CSL
(see Figure ), to quit the system, login, logout, and close all
windows but the Search Window. Other Utilities menus may include
options to close all windows, return to the Search Window (without
closing any windows), set permission levels (to read or write to
an object you have created), or print (effective only from Sun workstations
connected to a printer). Be sure to review the options available
from the Utilities menu. Click here for Picture
Adding Data and
Links
The archival data and literature for the worm has already been
placed into the information space for WCS. However, much of the
most useful knowledge is not in the archives of the stock center
or the genome project, but resides within individual laboratories
and the community folklore. Capturing this informal knowledge has
always been one of the primary goals of WCS and this release contains
new functionality in support of that objective.
You may add any piece of information whose type is known by the
system, e.g., 2 and 3 factor data, deficiencies, genetic rearrangements
(e.g., translocations), strain names, gene names, chromosomes, contigs,
clones, sequences, cells (lineage history), documents, images, persons
and labs. When you are finished entering the information, you can
publish it as desired. This publishing will permit you to restrict
new data to your lab, to collaborate with colleagues across the
country, or to distribute data to the community (or to a selected
portion thereof).
You may annotate information currently in the system. This feature
allows you to comment on current information. See the section on
annotations, page , below.
You may also create links between objects. We hope that you will
use this mechanism to record relationships between things, e.g.
potential locations of genes or hypotheses about functions. The
linking mechanism was designed to be very general so that you can
link anything to anything (any object(s) to any object(s)). The
sharing mechanism is intended to be symmetric with the browsing
function: the object being entered looks the same as the object
when retrieved later; links to other objects can be followed immediately
after entry.
Please note: If you are currently listed in the Persons list[2], your password has been set by CSL and you will need to
obtain it before you attempt to add new data. To obtain your password,
send email to wcs@csl.ncsa.uiuc.edu. In this release of WCS, you
will be able to change your personal data once you have received
your password. Because of the nature of passwords (they
grant "ownership" to individuals), you must personally
request your own password via email. We have no other consistent,
convenient, reliable method by which to confirm identities of individuals.
If you are not in the Persons list, see the sections on Logging
In and Passwords.
Logging In
Before you can add, change, or link an object, you must log in
to the system. Simply viewing data does not require logging in.
The Login command is nested in the Utilities menu on the Search
Window (see Figure ). Every object is owned by a "person"
in the Persons list. The owner can set the permissions for who else
may read or write the object. (In the case of data that has not
been added to the system by individual users, e.g., data imported
from ACeDB or other sources, the system owns the data, and therefore
the data cannot be changed by an individual user.)
When the Login command is selected, the Login window appears (see
Figure ). Find out if you are listed in the data. Enter your name:
Last-name <space> Initial(s).
Passwords
If you are listed in the Persons list, and you have received your
password from wcs@csl, you may enter that password. Passwords
are case-sensitive. You must enter your name as it appears
in the Persons list. Click here for Picture
If you are not listed, enter your name now, last-name <space>
initial(s). Enter a password. If you are not listed on the person
list, as seen in the Login window, you may set your own password.
The password is used later to check whether the current user is
an owner or has been given permission to read (display) or write
to (edit) an object. When you make up your own password (or change
your assigned password (see below)), CSL will not be able to determine
the password chosen. CSL can reset your password to a new password.
If you have password problems, please send an email message and
we'll work with you to restore your full access to WCS. After entering
your password, press enter or click Done.
If your name has not previously appeared, you will be given an
opportunity to complete further information about yourself, including
your email address, telephone number, laboratory affiliation, etc.
Once completed, the new data is linked to your name and is your
person object (see Figure ). After you have logged in, you can enter
new data, edit your own data, and create links between objects.
You will also be able to change your own person object. People listed
in the "Representative" field in the lab object have write
access to that lab object, and can therefore change mailing address,
name, etc.
Changing Your Password
You can change your password, whether you've made it up yourself,
or you've received it from wcs@csl.ncsa.uiuc.edu. To change your
password, login as usual, and retrieve your person object. From
the Utilities menu on your personal object, select Change Password.
Follow the prompts that appear.
Entering Data
Use the Type Selection menu (left side of the Search Window, under
Search This Type) to select the type of object to be created.
Once you have logged in, the New command button (on the Search
Window) will be active. When you click New, an empty object of the
specified type is created and displayed for data entry in a separate
window. For example, a gene object has the fields Name, Clones,
Sequences, and so on. To enter a value in a field, select the field.
A box or cursor will then appear in the field. You can now enter
the value in two ways.
Typing Field Entries
If you type text, the characters are entered and checked for validity
against the data type of the field when you press Return or select
another field. This is called type checking. If an invalid value
has been entered (a gene name instead of a clone in the Clone field),
a dialog box will appear. If the object is also a new object in
the information space, another window will open, allowing you to
enter that new data as well.
In the Name field if you type a name that is already defined, that
object pops up in a separate window. For example, in the Name field
of a Gene object, typing "mec-3" brings up the existing
mec-3 gene. Typing a new name defines a new gene object and enters
that name in the master list of all genes (thus you can find it
with the Locator box and through a string search in the Query Specification
box).
If the data you type in fields other than the Name field represents
another object, a link is automatically built between the object
you are creating and the existing object. The link can then be followed.
You may type multiple objects into a single field, presuming
the field supports multiple items, tabbing after you enter each
object. For example, you may add all of your lab members
to the Lab object: enter their names as they appear in the Persons
list, and between names.
Embedding Objects (Copy-and-Paste)
You can copy-and-paste (embed) current objects into your new object.
This method creates a link. Use the Type Selection menu and Browser
to retrieve data for this purpose. This method is particularly helpful
to readers of documents: the embedded object appears underlined
and italicized, drawing attention to the presence of a link. Click
here for Picture
Our example is gene: tes-1 (see Figure ). The name and the contents
of one field have been entered in the new object (TF2). To add another
field, Alleles, return to the Type Selection menu, select alleles
as the data type, enter the name of the allele in the Locator box,
and retrieve the object. In this case, we selected allele ad459.
From the retrieved object , (in our example, allele:
ad459) use the Display menu option, Copy. Choose Copy... This Object.
From the new object , select Paste from the Display
menu (see Figure ). The name of the allele will appear in the Allele
field. Click here for Picture
You can select more than one object to copy and paste. For example,
instead of re-keying all of an author's work, you could retrieve
the Person object of the individual which contains their Papers.
Select several papers; copy and paste them into the appropriate
field, Related Documents. These multiple objects are then embedded
in the new object. The new object is defined when you enter the
Name of the object and press Return or click on a new field. It
is saved into the information space and accessible in a variety
of ways. It can be retrieved via the Locator box. If a link has
been made to it (see below), that link can be followed to display
the new object. You may search for the object using a query.
Annotating Data
You may find data, including documents or biological types, which
you would like to annotate with a comment. You can annotate the
object by selecting Annotate from the Links menu. Log in first.
You can annotate the entire object, or a selected field within the
object (see Figure ). An annotation window will open, and you may
compose your annotation. You can change the annotation's title.
When you are finished, click Close on the annotation window. Click
here for Picture
Editing Data
If you own the data or have been given writing privileges to the
data by the owner, you can edit it. You can edit your personal information
as well (your Person object). First, you must log in. Then, retrieve
the data you wish to edit. Insert the cursor at the appropriate
field of the form, or line of the document, and begin typing. Insert
the cursor and backspace to delete text.
Fonts, formats, etc., have been standardized in each data type
to maintain consistency in displays across old and new data. The
defaults may not be altered. However, within your document, you
may change the size and style of the font. Click
here for Picture
Deleting Data
You may delete objects you have created. Log in and retrieve the
object. Drag down the Display menu to Delete. Choose ...This Object,
or, if you choose, you may delete selected fields within your object.
You will not be given a confirmation box, and any deleted
item is not retrievable.
Creating Links
You can also create connections in the information space. Connections
are made by creating links between objects. Links delineate an arbitrary
relationship between objects. For example, you can link a gene to
a document describing its function, link two similar genes together,
or link a gene to the set of clones that may contain it. See Figures
and .
Once created, user links (links that you create) can be followed
using the same navigation techniques as the system links (links
existing within the system). You can create links between the object
you create and objects currently within the system. You can also
create links between objects that currently exist in the system.
Links can be made between objects, or between parts of objects.
Links are bi-directional -- links starting at one object and finished
in another object can be followed from either object. Click
here for Picture
After logging in, the option, Start Link.... becomes available
on the Links menu (see Figure ). Start the link from the object,
or from a selected piece of text within the object.
Retrieve the object to link to. In Figure , a new link has now
been created, and will appear when links are shown or followed from
either object. Click here for Picture
Publishing: Controlling
Access to Your Data
You can control the extent to which your data is propagated to
the worm community by setting permission levels after you enter
your data. From your data on the screen, use the Permissions option
on the Utilities menu. The Permissions window appears (see Figure
). Once you enter an object into WCS, you are recognized by WCS
as the "owner" of that object. In keeping with the community/collaboratory
nature of WCS, all users have Reader Privileges to all objects
within the system, and to all objects that you enter unless you
(as the owner) restrict access ; see below. No users have
Writer Privileges to objects other than objects that they have personally
entered into WCS, unless permission has been explicitly given
by the owner of the object . This includes the permission
by the system to Lab directors, who may change lab information.
The owner has writing privileges to the data owned, and may permit
others to have "read-write" access. Writing privilege
implies reading privilege. Users at any site can be given Writer
Privileges -- you can collaborate with colleagues across the country.
Once access is restricted through the Permissions window, the object
is restricted from the rest of the users.
For example, if you enter a document and set Readers access to
include only your collaborators, no one else using the system will
be able to access your document: just you and your collaborators.
If you set Writers access to include your collaborators, the same
is true -- no one else, other than yourself and those you have designated,
may read or write to your document.
You may also set one group of people as Writers and a completely
different group as readers.
Levels of Publication
The technology is currently available within WCS to allow the community
to establish levels of publication: postings (simply adding data/documents
to the system), moderated (peer review or otherwise monitored publication),
or in the case of biological information, curated data. At this
time, the level of publication is posting. No editorial process
is currently implemented to support peer review, moderated entries,
or curated data. CSL is interested in working with members of the
community who are interested in utilizing the system in this manner.
Readers
Read-only access, the default level of access, is the attribute
given to all objects. Initially, all users can read all data.
This level of access allows users to search for, retrieve, and link
to the object. When links are shown from an object, the names of
all objects having unrestricted read-only access are listed in the
set.
Select the Readers' box to enter an X. Type a name (last name first)
in the box under People; the window below that box will scroll through
names. Either completely type the name or click on the name in the
People list; the name will be entered under the Readers list. Click
here for Picture
Writers
Persons to whom you give this level of access are allowed not only
to read, but to write to (amend, revise, delete)
an object you own . If the new object is linked to other
objects within the space, when links are shown from an object, the
`protected' data is not visible in the listing of links. A link
listing is stated, but your object appears as "unknown."
Enter Writers in the Writers' list by selecting from the People
list, as described above; make sure the Writers' box shows the X.
In Figure , Levezow, Opac, Riedinger and Wigglesworthy have been
given permission to write to an object by the object's owner. In
this case, only the owner of the object and these people may read
and write to the object. In addition, Dewey, Raganathan and Shera
may read the object. They may not write to it, however. A fourth
person is being added to the group of Readers.
All other users of the system are excluded from seeing, retrieving
or writing to the object. Click here for Picture
Changing Permission
You may decide, after collaborating on data either within your
lab or with a group of colleagues across the country, that you want
to broaden the level of access to your data. Retrieve your data,
and return to the Permissions screen. Remove any restrictions so
that no users appears under the Read column, and if you so choose,
no users appear under the Write column.
Only when there are no names under Readers or Writers will all
users of the system be able to view your data.
Appendix 1: Getting
and Installing WCSr2
The front end software, software shell scripts, and user documentation
are available in the public access area (anonymous ftp site) on
the CSL server, csl.ncsa.uiuc.edu (141.142.221.11). Please
get the latest README files when you get the software. The
README file contains helpful information and instructions for setting
up the software on your local machine. At the time of this
writing, the README file contained the following information.<>
Installation of the Worm Community System release 2:
On your Sun server:
- 1. ftp the binaries and associated files.
- 2. Move them into the account that you will run WCS out of.
- 3. Make the binary and shell script executable.
Make sure to use the binary transfer mode (type binary at the ftp
prompt.) After cd'ing into the /pub/WCSr2 directory type mget
* and then press return.
The ftp program will ask you if you wish to retrieve a file. Each
time it does type "y" and press return. A typical
ftp session might look like the following on a Sun machine named
WORMY
login: worm
password:
Last login: Fri Feb 18 13:26:30 from mac221-128.ncsa.
SunOS Release 4.1.1 (WORMY) #10: Fri Jun 12 12:48:27 MST 1992
wormy% pwd
/usr1/wormy/worm
wormy% ftp csl.ncsa.uiuc.edu
Connected to csl.ncsa.uiuc.edu.
220 csl.ncsa.uiuc.edu FTP server (SunOS 4.1) ready.
Name (wormy.powell.edu): anonymous
331 Guest login ok, send ident as password.
Password: [your email address goes here]
230 Guest login ok, access restrictions apply.
ftp>ls [list the files/directories on CSL]
200 PORT command successful.
150 ASCII data connection for /bin/ls (128.174.4.10,3575) (0 bytes).
WCSr2
bin
dev
etc
pub
usr
wormpics
226 ASCII Transfer complete.
47 bytes received in 0.14 seconds (0.33 Kbytes/s)
ftp> cd WCSr2 [change to the directory where WCS files
are stored]
250 CWD command successful.
ftp>ls [list files in the directory]
200 PORT command successful.
150 ASCII data connection for /bin/ls (128.174.4.10,3581) (0 bytes).
README
README.MacX.FONTS.txt
README.SOLARIS
README.XLIBS
WCS.macx
WCS.macx.hqx
alpha
cover.letter.txt
leon.wbgs.tar.Z
lib
print_this.sh
quick_start_postscript
quick_start_text
quick_start_word5.bin
users_manual_postscript
users_manual_text
users_manual_word5.bin
wcs.front_end
wcs.r2
226 ASCII Transfer complete.
312 bytes received in 0.089 seconds (3.4 Kbytes/s)
ftp> bin [change the transfer mode to binary]
200 Type set to I.
ftp> mget * [get multiple files]
mget quick_start.ps? y
200 PORT command successful.
150 Binary data connection for quick_start.ps (141.142.221.11,2358)
(864946 bytes).
226 Binary Transfer complete.
local: quick_start.ps remote: quick_start.ps
864946 bytes received in 1.2 seconds (7.3e+02 Kbytes/s)
mget quick_start.rtf? y
...
mget wcs.r2? y
...
ftp> quit
221 Goodbye.
wormy% ls [list the file in your local directory]
quick_start.ps quick_start.word wcs.r2
quick_start.rtf wcs.front_end
...
wormy% chmod +x wcs.front_end wcs.r2 print_this.sh [make
the binaries executable]
wormy% wcs.r2 [invoke the batch file that starts the system]
(the program runs, windows pop open...)
Printing from WCS: Choosing Print This from the WCS Utility
menus invokes a script named print_this.sh
This script prints from the Sun to the default printer
on that machine (the first printer in the /etc/printcap
file) -- the printer specified by $PRINTER (in Sun Operating System)
or $LPDEST (in Solaris). The default is printer lp. If you wish
to print to another printer you should edit the script and add:
PRINTER=<desired printer name>
Example:
PRINTER=lw0
export PRINTER
On Solaris systems use:
LPDEST=<desired printer name>
Example:
LPDEST=lablw
export LPDEST
Printing the documentation (on Suns) On SunOs type:
wormy% lpr quick_start.ps
wormy% lpr user_manual.ps
On Solaris systems use:
wormy% lp quick_start.ps
wormy% lp user_manual.ps
Running the WCS from a Mac You can also run the WCS on a Macintosh
using MacX xterminal software. The front end must still
be on a Sun. The file WCS.macx is a MacX file which does
all the necessary startup (i.e. double-click on the icon and it
will start up the system.) Remember to use the binary mode
in FTP when transferring to your Mac.
You will need to customize this MacX file to your local
setup.
When in MacX, select Edit Command on the Remote menu and double-click
WCSr2. Change the IP address after the -d to your IP address for
your Mac. (If you don't know this, select Control Panels under
the Apple menu at the top level and double-click MacTCP ).
Then click the Host button and change the top host number to
the IP address of your Sun running the front end (nslookup machine
name will print this).
Then issue Set within Edit Remote Command. Quit MacX saving the
changes and then you should be set.
Printing the documentation on Macs The user manual and quick_start
are in PostScript and ASCII files.
Remember to use binary mode when getting documentation files
via anonymous ftp.
Appendix 2: Users'
Tips & Resources Macintosh Monitors
I'm using a NEC MultiSync 5FGe Monitor with a Mac Quadra 650 (and
I use MacX for running WCS). It's 17", color (no. of colors
depends on video card in machine to which it's connected). NEC makes
several "MultiSync" monitors of various degrees of complexity
and ranging from 15" to 21". The 5FGe is one of the middle
range ones.
The key feature of the MultiSync monitors (what made one worth
an extra $200 over the Mac 16" for me) is NEC's "DPI-on-the-fly"
software (free from NEC upon request). This adds a control panel
that lets you change the screen DPI while the machine is running,
no rebooting involved. Thus you can go to 1024x768 for things such
as WCS that need to think they're on a big SUN screen, then return
to 832x624 or 640x480 (you have all three choices) for word processing,
etc., so you don't have to squint to read tiny letters. (Aside:
we have had some funky interferences between the DPI-on-the-fly
and one or two extensions/inits, but nothing disasterous.) To attach
the monitor to a Mac, all you have to do is request the appropriate
adaptor (also free) when you order the monitor. NEC has lists and
tables that show the compatibilities of various monitors and the
DPI-on-the-fly software with different Macs and PCs (try their FastFax
number to order FAX copies of information - I don't have the number
in front of me at the moment, but you can usually find it in the
ad sections of MacWorld, and probably other computer magazines as
well).
I've been quite pleased with the monitor so far, and the DPI-on-the-fly
has been a good solution to the display problems one often encounters
when trying to use a Mac as a terminal for an X application. (Credit
goes to Thomas Burglin for suggesting that I check into the MultiSyncs.)
Hope this is useful
-------------------------
Ann Sluder
asluder@zookeeper.zoo.uga.edu
Dept. of Zoology
University of Georgia
Athens, GA 30602
(706)542-3378
(706)542-4271 FAX
Leon Avery's WWW ServerClick here for Picture
The celegans mailing list and bionet usenet group: Date: Tue, 11
Oct 1994 11:55:26 -0700
Subject: Welcome to celegans
"To subscribe (depends on your location)...
. In Europe, Africa, or Central Asia, send the message
"SUB bionet-news.bionet.celegans" (no quotation marks)
to
MXT@dl.ac.uk
. In the Americas or the Pacific Rim, send the message
"subscribe celegans" to
biosci-server@net.bio.net
If you ever want to remove yourself from this mailing list, send
the
following command in email to "biosci-server@net.bio.net":
unsubscribe celegans [email address]
Information for CELEGANS/bionet.celegans
USENET name: bionet.celegans
Mailing list name: CELEGANS
Discussion Leader:
William Morgan
College of Wooster, Dept. of Biology
Wooster, OH 44691
wmorgan@acs.wooster.edu
CELEGANS/bionet.celegans charter:
Since Sydney Brenner's pioneering work in the 1960's, research on
the model organism Caenorhabditis elegans and related nematodes
has exploded. This rapid advancement has been aided in large part
by the extensive cooperation and open communication that has characterized
the C. elegans research community. As the number of C.elegans researchers
and laboratories continues to mushroom, I would like to propose
the formation of a new group devoted to research on C. elegans and
related nematodes. This newsgroup will help maintain the close ties
between all C. elegans researchers and will complement existing
avenues of information dissemination, including the biennial International
C. elegans Meeting, the Worm Breeder's Gaztte, and ACEDB.
Formation of this newsgroup will provide:
*** A source of quick help on specific methodological problems.
*** An additional forum for the discussion of ideas, problems and
recent developments on C. elegans and related nematodes.
*** A bulletin board for announcements pertinent to C. elegans researcher
(e.g., job positions).
*** An additional means for sharing strains, molecular reagents,
etc.
*** Further opportunities for collaborative efforts between labs.
*** A depository of practical advice and other information.
The newsgroup is unmoderated and William Morgan (wmorgan@acs.wooster.edu)
is the current
coordinator.
Appendix 3: Troubleshooting
PLEASE! remember to get and review all of the README files
from the WCSr2 directory! The following information, though current
at the time of manual publication (uploaded to the ftp site), is
subject to change without notice!
1. If it's taking a Long Time to search.....
There are several factors, local and regional in nature, that affect
the performance of the system in each lab. These factors include
the local hardware configuration and network at each institution,
the level of traffic on the Internet, and the nature of search or
retrieval being performed. For example, searching data for a broad
term that will retrieve hundreds of "hits" may take up
to a minute, perhaps longer, depending on various factors as indicated
above. Retrieving the cell lineage or other graphical displays will
take a minute or two if not longer, in part because of the size
of the data traveling across the Internet.
If you've just started (or restarted) the system, CSL is sending
your local machine some information; the amount of data may slow
down your initial queries. Five minutes or so after initial start-up,
the system should be running at normal speed. There will be some
lag time, because your queries are traveling to Illinois, and the
result of your queries travels from the server here as well.
After you have done a search, the results are cached locally, and
your manipulation of them (linking between found items, retrieving
objects from a set, etc.) should be relatively quick -- seconds
in retrieval time.
If you think your queries are taking longer than they ought, please
send us a note--wcs@csl.ncsa.uiuc.edu-- and let us know
a. what you were doing (or trying to do)
b. how long the response took (in minutes)
c. what you expected to happen (what has happened in your experience
with WCS)
The more you gripe to us with specifics, the better we will
be able to respond.
2. If WCSr2 doesn't display properly while using MacX, you may
want to try the following fixes:
add font aliases for fixed and fixed-13 (see the README file for
Macintosh fonts)
make sure your MacX has 4+ megabytes of ram to use
quit other applications to speed up MacX
3. You must have the SunOS 4.*.* binary compatibility package installed
to use WCSr2 with Solaris at this time.
4. If you cannot run the WCSr2 system and are experiencing errors
like: ld.so: libXext.so.4 not found, then you probably need to look
at your x-windows version.
If you use OpenWindows, look in /usr/openwin/lib. Under OpenWindows
it will tell you which version it is when it is started up.
For X-windows related stuff, look in directories in your system
named something like: /usr/lib/X11, /usr/local/lib/X11*. If any
of those exist and have libraries in them then check which version
they are. Under X11 the best way to determine this is by looking
at the library revision number of the X11 libraries. They should
be in the 4s and 5s (i.e. libX11.so.4.10) for X11R5. If you don't
see that kind of stuff, or if you're not sure what you're looking
at, try this:
Using anonymous ftp to csl.ncsa.uiuc.edu, get the X libraries in
the lib directory, which is in the main WCSr2 directory.
ls -l lib:
total 1720
rwxr-xr-x 1 root 458752 May 14 18:15 libX11.so.4.10*
rwxr-xr-x 1 root 245760 May 14 18:15 libXaw.so.5.0*
rwxr-xr-x 1 root 40960 May 14 18:15 libXext.so.4.10*
rwxr-xr-x 1 root 49152 May 14 18:15 libXi.so.4.10*
rwxr-xr-x 1 root 90112 May 14 18:15 libXmu.so.4.10*
rwxr-xr-x 1 root 294912 May 14 18:15 libXt.so.4.10*
You should place these libraries in a lib subdirectory in
the directory you are running the WCSr2 system from.
A typical installation might look like this:
wormy% pwd
/usr1/wormy/worm [directory where WCSr2 is]
wormy% mkdir lib [make a directory called lib]
wormy% cd lib [change to that new directory]
wormy% ftp csl.ncsa.uiuc.edu
Connected to csl.ncsa.uiuc.edu.
220 csl.ncsa.uiuc.edu FTP server (SunOS 4.1) ready.
Name (wormy.powell.edu): anonymous
331 Guest login ok, send ident as password.
Password: [send your email address here]
230 Guest login ok, access restrictions apply.
ftp> cd WCSr2/lib
250 CWD command successful.
ftp> bin
200 Type set to I.
ftp> mget libX*
mget libX11.so.4.10? y
mget libXaw.so.5.0? y
....
ftp> quit
221 Goodbye.
wormy% ranlib libX*
wormy% cd ..
wormy% pwd
/usr1/wormy/worm
Edit the wcs.r2 file (the script that starts WCSr2) using VI
or another text editor.
Edit the "setenv LD_LIBRARY_PATH /usr/lib/X11:/usr/openwin/lib"
line to read something like:setenv LD_LIBRARY_PATH /usr1/wormy/worm/lib:/usr/lib/X11:/usr/openwin/lib
The exact change will depend upon *where* the new lib directory
is in the system (i.e. where you installed it.)
Index
|
Access to your data
controlling 26
ACeDB iv, 1
Acknowledgements iv
Adding data 20, 22
Adding links 20, 24-25
Annotate 23
figure 23
see also, editing data 24
Anonymous FTP 28
Binaries 29
Biological data 8
Bionet usenet group 34
Boolean box
figure 14
Boolean logic (AND/OR) 15
Browser window
figure 6, 12
C. elegans mailing list 34
Cell lineage v, 12
figure 8
Cells v, 12
pictorial display 8
Changing permission 27
Client-server architecture 1
Clone
pictorial display 9
Close all windows 18
Community system 1
Community Systems Laboratory (CSL) iv, 1
Contents of WCS 1
Controlling access to your data 26
Copy 18, 22
Creating links 24
Cut 18
Delete 18
Deleting data 24
Display menu 18, 22
Displays of Types 6
Documents 6
Editing data 24
Embedded Objects 9
Embedding
multiple objects 22
Entering data 21
Copy-and-Paste 22
embedding objects 22
multiple names, single field 22
type field entries 21
Error messages 35
Ethernet 4
Field restriction menu
figure 6, 14
Figures, from documents 7
Figures, show 18
Finding things, how to v, 12
Forms 8
Graphic display 8
functionality 9
Gripe 18, 35
Hardware requirements 4
History
button, figure 6
menu, figure 16
How do I...
add data 20, 22-23
add links 20, 24
annotate 23
anonymous FTP 28
browse 12
change my password 21
configure WCS 28
control access to my data 26
copy and paste 22
create links 20, 24-25
delete data 24
edit data 24
enter data 21-23
find something I know the name of 12
finish a link 25
get my password 20
get WCS 28
login 20
logout 18
print 18
publish my data 26
quit 18
return to the Search Window 18
start the system 29
search v, 11, 13
search a subset of data 13
search one type of data 14
start a link 25
Images, from documents 7
Images, show 18
Information Space
figure 5
Interface 6
Internet resources 33, 34
Lab members
entering in field 22
Laboratory affiliation 21
ld.so: libXext.so.4 not found 35
Libraries
X-windows 35
Lineage button v, 12
Links 5, 9
creating 24-25
|
start to finish, figures 25
Locator box 6
figure 12
Login 18, 20Logout 18
Macintosh
configuration 31
fonts 35
node 31
problems 35
requirements 4
Mailing list, celegans 34
Multiple objects
embedding 22
in single field 22
National Center for Supercomputing Applications (NCSA) iv
National Science Foundation (NSF) iv
New 21
button, figure 6
Objects
embedded 9
ownership 26
types 5
Open Selected 18
OpenWindows 4, 35
X-windows 35
Ownership 26
Panel
button, figure 6
figure 14
Papers 22
Password 21
changing 21
Paste 18, 22
Performance 35
Permission
changing 27
Permissions option
utilities menu 26
Permissions window
figure 26
Persons list 20
Physical map
figure 9
Pictorial display 8
Print 18, 29
Publications
curated 26
moderated 26
posted 26
Publishing 26
Query specification box 6, 13
Quick start v
Quit 6, 18
Readers access 26
README 28
Related documents 22
Results of search
figure 9
Retrieve an object 25
Search
all of the data 13
browse 12
one type of data 14query 13
quick start v
subsearch 13
Search All 6, 13
Search strategies
Boolean queries (AND/OR) 15
short-cut 15
sophisticated searches 15
stacking queries 15
Search this Type 6
Search window
figure v, 6
Set 9
figure 9
Short-cut 15
Show images 18
Software platforms 4
Solaris 4, 35
SparcStation 4
Speed 35
Subsearch 13
search all of the data 13Sun workstation 4
System requirements 4
Thesaurus
button, figure 6
figure 16
Troubleshooting 35
Type restriction menu 6
figure 6, 14
Type selection menu 14
figure 6, 12
Types
data 5
displays 6
Usenet group 34
User status 20
Utilities
button, figure 6
menu, figure 18
World Wide Web, C. elegans site 33
Worm Breeder's Gazette 1
Worm Community System (WCS) iv, 1
Writers access 26
X-windows 4
Libraries 35
OpenWindows 4, 35
X11 4, 35
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[1We know of one site that has run the system
on 8 megs of RAM; it's not a pretty thing.]
[2Use the Type Selection menu (far left of
the full search window), to browse Persons. Type your last name
in the locator box to scroll the browser window to your area of
the directory.
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