Genemapper

From Carl R. Woese Institute for Genomic Biology - University of Illinois Urbana-Champaign
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About

GeneMapper® Software is a flexible genotyping software package that provides DNA sizing and quality allele calls for all Life Technologies® electrophoresis-based genotyping systems. Genemapper Website

The GeneMapper Remote Desktop is shared among all of the researchers who make use of our facility for fragment analysis applications. Before setting up your initial connection to the desktop, and each subsequent time you access it for data analysis, you must schedule a session on our Online Calendar at http://www-app.igb.illinois.edu/biotech_schedule/.  Sessions are limited to 4 hours per customer per day.

Please follow the steps carefully and do not skip any of them. If you have questions or problems, please contact us at dna-seq@illinois.edu or 217-333-9520.

Access

Reservations

After you receive confirmation that your Genemapper account has been set up, you may log on to our online calendar and reserve a time slot. To schedule a session, go to the online calendar at http://www-app.igb.illinois.edu/biotech_schedule/.

  • After signing in, click on the "Schedule" tab, "Bookings."
  • Double-click on the box that corresponds to the time and date that you want to use Genemapper. All times are CST. You can choose up to four hours a day.
  • Choose only one server: either "Genemapper - Remote 1" or "Genemapper - Remote 2.." Do not sign up for both at the same time.
  • When you double-click your choice of time, you can create a reservation. Choose your "Begin" time and your "End" time. Click "Create."
  • Click the "Sign Out" link at the top right of the page.

Connecting

Genemapper Servers

  • genemapper1.biotech.illinois.edu
  • genemapper2.biotech.illinois.edu

IMPORTANT NOTICE TO ALL OFF-CAMPUS USERS

There is currently a security issue with off-campus users using Remote Desktop Connection. Here are instructions on how to connect to the Genemapper servers when you are off-campus. These instructions are only temporary. Sometime in the new year, we will probably be setting up a VPN server and then shutdown this method.

1. Go to https://remote-gateway.igb.illinois.edu/guacamole/ and login with your username (netid only - not the "IGB\" part) and your password.

2. There should be a "Genemapper" listed under 'All Connections'. Select the plus sign.

3. Then select genemapper1 or genemapper2.

4. This opens a remote desktop session inside the web browser. Login as you normally would.

5. Now you can go straight to the #Running_Genemapper_Software section.

Windows 8/10

  • Launch the Remote Desktop Connection client by typing "Remote Desktop Connection" in Search. Click on "Remote Desktop Connection." The RDC dialog box will appear.
  • Follow the same directions as listed below for Windows 7, as the Remote Desktop Connection program has not changed from Windows 7.
  • Be sure to read "Running Genemapper software" for instructions on important first-time use of the Genemapper software.

#Running_Genemapper_Software

Windows 7

  • Launch the Remote Desktop Connection client. Go to the Start button, then All Programs> Accessories> Remote Desktop Connection.
  • In the "Computer" field, enter "genemapper1.biotech.illinois.edu" or "genemapper2.biotech.illinois.edu" DO NOT CONNECT YET!

ConnectToGenemapper W7.png

  • Click on the arrow next to "Options." It should expand to a window with several tabs.
  • Now you will set up your connection preferences.
  • On the "General" tab: Enter IGB\ and your username in the "User name" field. This will be IGB\[your netid] if you are part of the U of IL campus, or IGB\cbc_[username] if you are outside campus. You will be asked for credentials when you connect.

RevisedGeneralTab.png

  • On the "Display" tab: Choose "Large" for the full-size remote desktop screen. Choose "Highest Quality (32 bit)" for the colors. If your computer seems really slow, you may want to change this setting.

DisplayTab RDC W7.png

  • Skip the "Local Resources" tab. See #Transferring Data for optimum results in working with your data.
  • Click on the "Experience" tab and under "Performance," select your connection speed (i.e., dial-up, LAN, etc.) Choose LAN for use here on campus.

ExperienceTab Performance Connection.png

  • Now you can click the "Connect" button. The GeneMapper server will open. Read "Running Genemapper Software" for important instructions on first-time use of Genemapper software.

#Running Genemapper Software

  • At the end of your session, first exit out of the GeneMapper software and then log off from the remote server. Please note that if you simply close the remote window you will not be logged off and others will be prevented from accessing the computer.
  • In the remote window, go to Start> Log Off.

OS X

  • If you don't have Remote Desktop Connection for Mac, you can download it here: http://www.microsoft.com/en-us/download/details.aspx?id=18140
  • When it is installed, before connecting to the GeneMapper server, go to the top left of your screen to set up your connection preferences. Click on RDC > Preferences. It should open a window with several tabs.
  • On the Login tab:
    • Enter your username in the User name field. Your username is IGB\[your netid] if you are on campus, or IGB\cbc_[username] if you are outside campus.
    • Enter your IGB password in the Password field.

RevisionOnUsername.png

  • On the Display tab:
    • Choose ‘1024 x 768’ for the size of the display to obtain the best performance.
    • Choose 'Thousands' for the colors.  'Millions' will slow down the connection to the remote computer.

Screen shot RDC Mac.png

  • Skip the "Drives" tab. See #Transferring Data for optimum results in working with your data.
  • Now type "genemapper1.biotech.illinois.edu" or "genemapper2.biotech.illinois.edu" in the Remote Desktop Connection for Mac window and click "Connect"

Screen Shot 2014-04-14 GenemapperSrvr Mac.png

  • If you get a dialog box warning you that the server name on the certificate is incorrect, go ahead and click "Connect."
  • If you get a dialog box warning you that the identity of the computer can't be verified, go ahead and click "Connect."
  • Click "Ok"
  • Launch the Genemapper 5 software.
  • For important instructions on first-time-use of the Genemapper software, read "Running Genemapper Software" below.
  • Please remember to keep an eye on the time.
  • When you are finished, exit out of the Genemapper software. Then log out of the Remote Genemapper. Please do not just close the remote window; you must click on the Start button, and "Log off" or you will prevent others from accessing the computer.

Running Genemapper Software

  • Double/click the shortcut on the desktop for the Genemapper software.
  • If your name is not available using the drop down arrow beside "User Name," type your netid or "[cbc_username]"
  • Type your temporary, one-time password, "biotech" You will get a message telling you to change your password, and the "Change password" dialog box will come up. Type in the password you wish to use; click OK.
  • The Genemapper software will open.
  • At the end of your session, first exit out of the GeneMapper software and then log off of the Genemapper computer. Please note that if you simply close the remote window you will not be logged off and others will be prevented from accessing the computer.
  • In the remote window, go to START > Log Off.

Transferring Data

  • If you are part of the University of Illinois, use U of IL Box to transfer data; otherwise use Dropbox or another system. Upload your data to U of IL Box and then download to a folder in Remote Desktop for analyzing. Here is a link to U of IL Box: https://uofi.account.box.com/login/. Another alternative is to use WinSCP, which is installed on Genemapper. It can be used to transfer data to and from an sftp/ftp server.
  • Please remember to keep an eye on the time!
  • Also, when finished, be sure to archive copies of your GeneMapper projects in U of IL Box or whatever system you are using. We have unfortunately had instances in the past when the Remote became corrupted and all data was lost. Please do not use the Remote Desktop as an archive for your files!