New version of the RESEARCH INTERFACE

Gary R Noonan carabid at CSD.UWM.EDU
Thu Feb 2 16:33:03 CST 1995

        Thanks to Jim Beach a new version of the RESEARCH INTERFACE is
available from the Taxacom FTP site.

        The RESEARCH INTERFACE is a stand-alone IBM compatible DOS program
written to:(1) speed up the recording of research specimen data; (2) help
the checking of research specimen data for accuracy; (3) produce specimen
databases suitable for use in GIS type software; (4) and to help the
analysis of systematics research data. The most current version is 1.8,
released January 1995. The current version includes several features not in
the earlier version put on a FTP site at Harvard and one at the University
of Ulm. The most notable new features are printer drivers for several
hundred printers and the ability to browse a database of populated places in
the United States, with each record listing latitude and longitude for each
such place and various other data.

        The material below is about the program and is organized into the
following sections:-- with long lines of asterisks separating the secretions.

        1. Directions for obtaining free copies of the program and manual
via FTP and for installing it.
        2. Background information about how the program came to be and the
rationale behind writing it.
        3. Major features of the program.
        4. Introductory section from program manual--giving more information
about program features.
        5. Plans for enhancing the program.
        6. Hardware requirements.

 Please feel free to contact me via E-mail with suggestions for program
enhancements or for questions.

                     *  Gary Noonan                         *
                     *  Curator of Insects                  *
                     *  Milwaukee Public Museum             *
                     *  800  West Wells Street              *
                     *  Milwaukee Wisconsin 53233  USA      *
                     *  and Adjunct Associate Professor     *
                     *  of Zoology                          *
                     *  University of Wisconsin-Milwaukee   *
                     *  carabid at                 *
                     *  voice (414) 278-2762                *
                     *  fax (414) 223-1396                  *

1. Obtaining the program via FTP

        The Research Interface program and U.S. latitude and longitude
database are available via FTP from the Taxacom FTP server at Cornell
University. The program and
files are in a directory  /pub/software/resint.

        To access the files, start FTP from your computer. Then use the open
command to access the  Taxacom FTP server. From my computer the command
sequence is as follows:
ftp {press the Enter key
open {press the Enter key}

 The FTP server will ask for your name. Reply anonymous and press the Enter
key. The FTP server will ask you to enter your complete E-mail address as a
password. Once this is done and you are in the system, type the following
cd pub
 Press the Enter key.
Type cd  software
Press the Enter key.
Type resint
Press the Enter key.

You should now be in the resint subdirectory which contains only files for the program. You
will need all of these files which in most cases are zipped.
        You must change to binary mode before getting the files.

Type binary and press the Enter key. You can then get the files by typing
mget * and present the Enter key.  If you don't want to have to confirm that
you want each file before it is sent, type prompt and press the Enter key
before doing the mget.

                   Be sure FTP is in binary mode
           before getting the files.
                To install the program make sure you
           have all its

                The manual for the program is supplied
           currently in the following files and
           doc60w.wpd The WordPerfect for Windows
              6.0a format in which the manual was
           docw51.doc    The WordPerfect 5.1 for DOS
                 version of the manual.If you
                 decide to print this document,
                 check the table of contents to be
                 sure that page numbers are accurate.

           docami3.sam  AmiPro 3.0.  I don't know how
                 this will look because I don't have
                 this program and had WordPerfect 6.0a
                 export  to this format.

           docww2.doc Microsoft Word for Windows
                 2.0c. Same comments as for
                 AmiPro format.

           ascii.doc Ascii format.  If you print this from DOS
                 you will have to number pages.  The table of contents
                 doesn't have page numbers because it is impossible to
                 know what they should be.

               Installing the RESEARCH INTERFACE

               Change to the root directory by typing
           <cd\> + <Enter>. Create the RESEARCH
           directory by typing <md research> +
           <Enter>. Change to the RESEARCH directory
           by typing <cd\ research> + <Enter>.
                FULL OR PARTIAL INSTALLATION  You may
           make a full installation which requires
           approximately 45 megabytes of hard disk
           space after installation. This option
           installs the places database which contains
           latitude and longitude for populated places
           in the United States. The full installation
           allows checking of latitude and longitude
           for U.S. populated places, automatic
           insertion of degree data into your research
           records and browsing of the places
               The option of a partial  installation
           does not install the places database. The
           partial installation allows you to use all
           other features of the program than  those
           associated with the places database.  A
           partial installation requires only
           approximately 7 megabytes. If you are
           working with foreign insects exclusively or
           lack adequate disk space, you may wish to
           make a partial installation.
               Copy the files from Internet into the
           RESEARCH directory and then type "install"
           and the <Enter> for a full installation or
           type "small" and the <Enter> for a partial
           installation. The installation program will
           make a subdirectory called GIS to hold
           files created for GIS software will make an
           export subdirectory to hold exported files,
           will make an import subdirectory to hold
           files to be imported  and will install the
           program for you.
               The full installation program will
           unzip all files while the partial
           installation will unzip all but the places
           database. During a full installation the
           install batch file will first unzip files
           and then issue  a command which starts a
           small program that builds an index for the
           large places database. The program  will
           show a small window in which somewhat
           cryptic information appears about index
           building. This window is provided so that
           you won't think nothing is happening while
           the index is being built. Depending on the
           speed of your computer and memory, building
           the index may take 15 minutes to an hour or

                Your next step should be to print a
           copy of the manual and then follow its
           directions for starting the program.

2. Background information about development of program and its rationale.

  Approximately two years ago I decided to use GIS type programs in
making geographical distribution maps and in analyzing geographical
relationships of carabid beetles on which I am doing monographs. This
meant that I needed an easy way for determining latitude and longitude
for specimens borrowed from other museums. I also decided that I needed
a program that would speed the entry of geographical and character state
value by research assistants and which would at least partially
automatically check their data entries. Over time I wrote and kept
augmenting a program. Once the initial goals were met I began to add
various features for further speeding data entry and for analyzing data.
The major current features of the program are listed below. I will be
happy to have the program distributed to people who think it may be of
use. For want of a more catchy name, the program is called the
         Once I have received comments from colleagues, I'll seek funds for
further program development. An important such development will be the
production of CD-ROM disks containing latitude and longitude and other
data for all countries of the world. The program will be modified so that
batch checking (see below for information about checking) can be done to
obtain latitude and longitude for records in research databases.
If development funds are obtained, the program will be greatly enhanced as noted below
and distributed at no cost or at  very low cost of  CD-ROM media.

    BASIC PHILOSOPHY Systematists should not have to become
expert in running a general database program to speed the recording of
research data and production of data files suitable for import into GIS
type software.  They should also not have to waste time examining
database records and manually producing a list of specimens examined.
Instead the systematist should be able to select menu choices to perform
these and other operations. The program includes a detailed manual.

        The files are zipped with the latest version of PKWARE. The files can include
the PKWARE program for unzipping files because I have a PKWARE
distribution license. The files when zipped require approximately 6
megabytes of space. The single largest zipped file is 2.7 megabytes. I can
distribute the program by disk but don't want to sit by the computer and
copy disk after disk.  If people want the program by disk, I'll have to
calculate a small charge to hire someone to copy disks, mail disks, and to
cover cost of postage and handling.

I can be reached at the Internet address of
carabid at or by snail mail at: Gary Noonan, Milwaukee
Public Museum, 800 West Wells Street, Milwaukee Wisconsin 53233.
telephone 414 278-2762

 3. Major features of program.
        Automatic insertion of latitude and longitude into current record for
records    containing a populated place in the United States. The program
will    also insert missing geographical data in many instances. For
example,    if you enter "Washington " in the state field and "Seattle " in
the    reference point or locality field, the program will insert the latitude
  and longitude into the current record. It will also insert "King " into
the county field, and if there is a known elevation for Seattle will also
insert that into the current record. These actions are done when the
user elects to check the data in the current record.
        Automatic calculation of total number of specimens. When the user elects to    check data the
program also adds the number of males and females    and inserts the
resulting number into the field for total number of    specimens from a
given locality.
        Checking of geographical data. When the user elects to
check a record, the    program also checks spelling of certain geographical
data for United    States localities. (Future program versions will check
spelling for    other countries. )
        Automatic checking of entry of geographical data. A common typing
error is    to accidentally press the space-bar before typing in the name of
a    geographical locality.--at least my typists do this. When the typist
moves to another field or another record, the program automatically
removes the initial space. The current version of the program also
capitalizes the first letter of the first word in certain geographical    fields.
(Future program versions will allow user to turn off the    capitalization
feature. ) For example, if the typist enters " seattle", the    program will
convert this to "Seattle".
  The program contains a set of 5 data screens for recording as much or
as little information about specimens as the user desires. Movement
between screens is by pressing the Page-Up or Page-Down keys. The
screens have fields for:   Species. This field records the species name (or
any temporary name selected    by user for a morph).
        Fields for entry date of record and for typist. These fields are helpful in
  tracking down problems in data entry.
        Specimen number field and site number field.
        Storage unit number field. Assigning a number to a storage unit and    recording such number makes it easy to locate
specimens.   Three tag boxes. The user can check 1 or more of these boxes
to tag a    record for later retrieval, printing etc.
        Data Checked Box. The program automatically checks this box after the    user has the program
check the data.
        Marked for Deletion Box. The user can check this box
and can (from the    Main Menu) delete all marked records.
        Geographical data--several fields (country, state or province, county or other    political
area, forest or park, reference point, distance in kilometers    from
reference point, local point [particular place or spot at reference    point],
elevation in feet, elevation in meters, latitude and longitude    [in decimal
form because such form works best with GIS software]).   Faunal faunal
field, with popup of faunal regions. User can modify the    regions listed
in popup.
        Field for source of latitude and longitude data. This field is a column of
  various data sources with parentheses by each data source. The user
checks the appropriate parentheses and thereby provides information
about the accuracy of the data.
        Fields for numbers of specimens: number of males, females, unsexed    specimens, immature males, immature
females, unsexed immatures,    total specimens.
        Field for museum and field for museum codon. Entry into the museum
field    activates a popup. Selection of a museum from the popup results
in    the program entering the museum name and codon into the
appropriate fields. The user can modify the museums and codens
presented in the popup and thus create a popup for his / her area of
        Fields for capture dates. There are two sets of fields in case the
specimens    were taken from a trap and the user wants to give the range
of dates.    For specimens collected on a given date, the user simply enters
the    date into the first set of date fields.
        Collector (s) field.
        Label data field. This field allows the user to enter miscellaneous label
        Ecology field. The user can enter detailed ecology data.
        Notes field. The user can enter notes about the current record.
        Biotype field. This is for recording data such as biome or plant community.    A related
field contains modifying terms for the biotype. Future    program versions
will allow the user to customize these fields.
        Fields for character state data. There are 20 numeric fields in which the user    can record numeric
states of characters for specimens being entered    in a record. The user
can define labels for each of the 20 fields for    each species. In other
words, the character state labels can be    different for different species
or can all the the same for a given field.    These fields are useful when
using GIS software. For example, one    might label the first field as
"Sclerotized ligula on internal sack of     internal sack" and assign
numbers to various character states. The    user can then have GIS
software display different symbols for sites    with specimens having
different character states. While the 20 fields    were originally conceived
for character state data, the user can label    them for other uses and
assign numeric values accordingly.
  The EDIT MENU is the menu normally visible when adding or editing
records. Features include:
  Add. Add a new record.
  Menu choices for viewing previous record, next record, first or last
record.   Print current record.
  Automatic entry into new records of user selected data. The user can
elect to    have the program automatically enter into new records data
such as    country name, state, county, museum etc. This speeds the entry
of    partially similar records.
  Choices for searching for particular records. Future versions of the
program    will contain additional choices allowing the user to easily build
a    customized search statement.
        Order. The program has numerous choices for selecting the order in
which    records are displayed.
        Filter. The user can decide to view only those records meeting selected
        Calendar / Diary. This feature allows the recording of notes and
association    of such notes with a particular day.
        Calculator. This operates similar to a hand held calculator.
        Convert regular degrees into decimals. Selection of this feature results in the    program presenting a
conversion screen. The user enters the latitude    and longitude and
directions (N,S,E,W). Choices are to convert to    decimals and show
results in conversion screen, cancel conversion, or    convert to decimals
and insert into current database record.
        Change species name automatically entered into new records.
        Convert miles to kilometers. The
program presents a conversion screen. One    choice is to do the
conversion and have the program insert the    number of kilometers and
the km abbreviation into the distance field    of the current database
        Convert GPS degrees into fully decimal degrees. Many GPS units
provide partially decimal degrees, giving degrees and minutes and
decimal subdivisions of minutes. The program can convert and insert
  converted values into latitude and longitude fields.
        Convert U.S. topographic map distances into decimal degrees. On certain    types of
topographic maps the user can measure distance from    nearest degree
line, enter distance and direction into conversion    screen and have
program calculate decimal latitude and longitude and    insert into
appropriate fields. An algorithm takes into account the    change in
spacing between degree lines as one moves northward or    southward.
        Copy, cut and paste data from field to field.   Undo and redo actions.
        Insert foreign characters. The program can insert many foreign
characters and will sort correctly on such characters.   Automatic pop-
ups. When the user enters various fields, the program    presents a popup
of choices. The user can select a choice and have    the program enter that
into the field or can enter a choice not in the    popup. The user can
modify pop-ups from the MAIN MENU.
  The MAIN MENU is the first menu in the program. The user can easily
return to this menu. Features include:
        Analysis of data. This choice produces a submenu.   View or edit text
files created by the program.   Generate lists of records by elevation.
Generate report listing for each species the numbers of males,     females,
unsexed specimens, immature males, immature     females and unsexed
immatures. The report presents these     numbers for each species by
month and also presents for each     month the sex ratio of captures. The
report also gives the     total numbers of the above statistics for each
species (totaling     the results for all months and for records without
month     entry).
        Generate restricted reports. The program produces reports for
subsets of records.
        Reports for ecological data, for records with data in notes or label
data fields.
        Check numeric data. The program checks numeric data in records
and lists those records with problems.   List specimens examined. The
program scans the entire current     database and produces an ASCII text
file that can be     imported into a word processing program.   List unique
sites in database.
        Analyze shared sites. The program can produce a written report or
an ASCII file that either lists all sites and their species or that     merely
provides summary statistics on the numbers and     percentages of sites
with one species, more than one species     (any number of species above
one) and sites with 2 or 3 etc.     species collected at them. This can be
useful in examining     sympatry.
        Produce reports listing the number of species per country, state or
faunal region.

  Utilities. Selection of this choice produces a submenu for obtaining
information about memory use by the program or modifying the    various
popup lists used by the program.
        DATABASE. This selection provides choices for: changing to another    database; removing all deletion marks
from records; deleting records    marked for deletion; creating new
databases; reindexing databases;    searching the places database; and
creating files for import into GIS    programs. The creation of GIS data
files allows the choice of    creating a separate data file for each species or
a single file for all the    species.
MENU   Both menus allow the user to search the places database which
contains records for 124, 444 populated places in the United States.

4. Introductory section from program manual.
  Purpose of program.
  The purposes of the RESEARCH INTERFACE are: (1) to speed the
recording of geographical data about research specimens; (2) to improve
the accuracy of such recording; (3) to provide tools for analyzing research
data; and (4) to produce files suitable for import into GIS (geographical
information systems) software.
  Conventions in identifying keys to be pressed.   In this overview and in
the manual keys to be pressed are surrounded by angles (< >). For
example, <Enter> means press the Enter key. The combination <Ctrl>
+ <a> means the user should hold down the Control key and press the
letter "a" key.   Getting started.
  For a quick overview, do the following. Change to the directory
containing the RESEARCH INTERFACE. Type < RESEARCH> and
press the Enter key. Select any typist from the list that appears. Select
the database "DEMO" from the list of databases. Pick any species from the
list of species the program presents.
  These steps will take you to the main menu. The top choices in menus
may be selected by clicking on them with a mouse or holding down the Alt
key and pressing the hot key which is in a highlighted color.
  Program check of locality data.
  Select the choice of Add (<Alt> + <a>). This adds a new record to the
database and presents you with the first of 5 data screens for that record.
Put the cursor in the country field (by clicking on that field with the
mouse or using the <Tab> to move forward and the <Shift> + <Tab>
key to move backward a field). The program will present a Pop-up list of
countries. Press the letter "U" to move to countries being with that letter.
Double click on "United States" with the mouse or move to that entry with
the arrow key and press the Enter key. The program will insert "United
States" into the country field.   Move to the state field. Select
"Washington" from the Pop-up of states by double clicking on it with the
mouse or moving to it with the arrow keys and pressing <Enter> when
"Washington" is highlighted. Move to the reference point field and type in
"Seattle". Press <Page-down> to move to the second data screen. Enter
the number 5 in the field for numbers of males and the number 44 for
number of females. Press the <Page-up> to return to the first data
screen. Select the CHECK choice from the top menu. This choice produces
a submenu. Choose the "Check all" choice. The program will search an
electronic database of populated places in the United States and will
automatically insert the county, latitude and longitude for Seattle. The
latitude and longitude are in the decimal form required for GIS software.
Press <Page-down> key for the second data screen. Note that the
program has totaled the number of specimens.   The program presently
can only insert data for populated places in the United States. Future
versions will handle data about all known place names (mountains,
springs, valleys, towns, lakes etc.) for the United States and other
countries. Future versions will also be able to calculate latitude and
longitude based on user specified distances from place names.
  Use of Pop-ups prevents the misspelling of geographical terms. The
program has various other features for preventing misspelling. For
example, two common typing errors are to type a space before the first
word in a field or to fail to capitalize the first letter of a geographic name.
  Move to the reference point field. Delete the data there by pressing the
key combination of <Ctrl> + <a> to select all data in the field. Press
<Delete> key. The field should now be empty. Type several spaces at the
start of the field and then type the reference point of "seattle". Now move
to another field. Note that the program automatically removes the leading
spaces and capitalizes "Seattle".   Below are some other suggested actions
for demonstrating program features.
  Speeding the entry of records with partially similar data.   The user can
have the program automatically insert repetitious data into new records.
To illustrate this choice, first enter some data in the fields for COUNTRY,
STATE, COUNTY and REFERENCE POINT. The "Set" choice of the top
menu allows the user specify which values to automatically enter. Select
this choice by using the mouse or pressing <Alt> + <s>. The resulting
submenu allows you to have the program take values from the current
record or from a screen for recording desired values to have repeat. Select
the choice of "Take sets from current record". Add a new record by
clicking on the "Add" choice of the menu or by pressing <Alt> + <d>.
Note that the new record has the geographical information you entered
in the previous one.
  Finding already entered records.
  Select "Find" from the top menu. From the first submenu select "Seek".
Pick "By data other than species" from the resulting submenu and then
select "Reference point" from the next submenu. A screen will appear for
you to enter the desired reference point. Type in "Milwaukee" and select
the choice below for seeking records with that reference point. The
program will find the first record for Milwaukee and will put records into
order by reference point.
  Analysis of data.
  Most analysis features remain to be entered and will be incorporated
into future versions of the program. However, the program currently
includes a routine for building files listing specimens examined, generating
reports about sites with more than 1 species collected at them [This
introductory section is somewhat outdated, there now are more analysis
features.] If you are
in the edit menu, go to the MAIN MENU by clicking on "Main Menu" or
by pressing <Alt> + <m>. Once at the MAIN MENU click on "Analysis"
with the mouse or press <Alt> + <n>. Select the choice of building lists
for all records in the species database. You will then see a submenu with
10 choices. Only the first choice is currently enabled. This choice will
build a file containing a list of specimens and associated geographical and
other data. The RESEARCH INTERFACE will search the database and
combine records with identical geographical information and total
specimens as appropriate to produce a list suitable for import into a word
processing program.   Because the ASCII values of and   also represent values associated with control items, files containing these
symbols will not import properly into most word processing programs. The
RESEARCH INTERFACE therefore uses symbols that can be imported
into word processing programs and easily converted into the and   symbols. (Use replace feature in word processing program to convert "m*"
into , "mm*" into , "f*" into   and "ff*" into   .) The resulting file follows a format that takes account of changes in
geographical information and month of collection. If funds are obtained
for further developing the program, many other formats will be added,
including ones that take account of other fields such as day, year,
compound collecting dates spanning an interval of time, museum and
collector.   To produce a list of specimens examined select Format 1. The
program will ask you for the name of the desired output file, will check
to be sure such name is not already used for another file and will create
a file based on records in database. A "thermometer" will show progress
in constructing the file.
  You can view the resulting file by selecting the "View/edit text files"
option of the "Analysis" menu. The program will present you with a list
of text files (those with a ".txt" extension) in the directory containing the
program. Use the mouse or arrow keys to highlight the desired file and
then press <ENTER> twice or use the mouse to click on the "Open file"
bar. The file will be displayed in a window whose position and size can be
changed as desired. To bring the window to maximum size, click on the
small yellow colored rectangle in the upper right hand corner of the
window's border. Clicking again on the rectangle again will make the
window smaller. If you click on the small yellow colored dot in the lower
right hand corner of the window's border and hold down the mouse
button and move the mouse, you can change the window size. To move
the window, click on the top border, hold down the mouse button and
move the mouse. The window can be reduced to a single bar with the file
name by double clicking on the window's top border; double clicking on
the border will reopen the window. To close the window, click on the
small yellow rectangle in the upper left hand border edge. If the file
contents don't fit on a single page, you can scroll upper or downward by
using the upward and downward pointing arrows along the right edge of
the window. To use these arrows, click on one of them and hold down the
mouse key until the desired text is displayed. You can also use the
keyboard up and down arrows to cause text to scroll up or down.   The
program also includes a feature for examining the sharing of collecting
sites by different species.--This recently added item is described above
under features.

  1. Develop CD-ROM disks containing latitude, longitude and other data
for   populated places and feature names of other countries. Make slight
 modifications to program so that user can browse such disks and so that
the   program can batch check records or separately check them (as at
present). The source of data for the CD-ROM disks will be from the already
published CD-ROM disk with approximately 2.2 million feature names for the
United States and a set of CD-ROM disks that will soon be released by the
federal government for other countries.

  2. Further develop the data analysis features of the program
according to   suggestions to be received from colleagues.

3. Purchase a commercially available and royalty free module (written in FoxPro) so
that users can interactively build statements or queries for selecting
records   to view, print or otherwise handle. I could easily write such a
module, but   this would be very time consuming. The commercially
available module   works well and supports a wide variety of queries and
can generate SQL   statements.
  4. Develop on-line help for program use.

  5. FoxPro is easily ported onto different platforms. The program can be
easily   modified for use on DOS based computers (current version is DOS
based),   on Unix based computers, on computers running Windows and
on   Macintosh computers.

  6. Further develop the "source" field for recording best information about
accuracy   of latitude and longitude data, per suggestions from colleagues.

 7. Set up a module that can calculate latitude and longitude based on a
specified   distance and direction from a place whose latitude and
longitude are known.

8. Implement other suggestions per future comments from colleagues.

9.  Install module for interfacing with bar code reader.

10. Develop a module for viewing data put into the RESEARCH INTERFACE by a
researcher. The module will provide viewing capabilities only and will allow
the user to easily search the database and to produce print outs of various
combinations of data. With this module researchers will be able to make
systematics data available to a much larger community, such as biologists
interested in environmental studies.
        For example, I am completing a monograph on the Holarctic  subgenus
Anisodactylus (genus Anisodactylus: Coleoptera:Carabidae;Insecta). This
group of insects is primarily found in wetlands. The database I've built of
geographic localities and ecological data may be of interest to
environmental biologists and to agencies such as the National Biological
Survey. The viewing program module will actually be a separate program
without the large databases of latitude and longitude for populated places
in the United States. By zipping the program and the Anisodactylus database
(approximately 11, 000) records [program refers to cut down viewing program]
I will have a small set of zipped files that can be distributed on disk
 or via FTP along with my forthcoming monograph of the group. Readers can access the
database--perhaps a good solution to the problem of what to do when funds
prohibit the publication of lengthy lists of specimens examined. The zipped
files can themselves be sent to environmental biologists or other interested
parties. Note however that increasing development of Worldwide Web may make
this feature unimportant except of course that searching records on a host
computer elsewhere is often slower than searching them on your own machine.

11. Develop a module for exporting research databases into a format that
gophers can use, providing users with another means of accessing detailed
geographic and other data usually not available to colleagues.

  The program is a DOS program but can also be run under Windows. The
program has been run here at MPM on a 486 computer with 48
megabytes of memory, on 386 computers with 4, 6 and 10 megabytes of
memory respectively. It probably will run on a computer with as little as
1 or two megabytes but will be slower than on computers with more
   A printer driver included with the program allows the user to select from
several hundred different types of printers.

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