Difference between revisions of "Genemapper"

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(Created page with "_TOC_ 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. #The GeneM...")
 
(→‎Connecting to Genemapper Computer)
 
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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.
 
  
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#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/genemapper/.  Sessions are limited to 4 hours per customer per day.
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== About ==
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GeneMapper® Software is a flexible genotyping software package that provides DNA sizing and quality allele calls for all Life Technologies® electrophoresis-based genotyping systems. [http://www.lifetechnologies.com/order/catalog/product/4475073?ICID=search-4475073 Genemapper Website]
  
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To schedule a session, first go to the Online Calendar and register. You’ll be granted access to the calendar when I confirm that you are a UIUC customer (I try to do this as soon as I receive the e-mail request). After you receive confirmation, you may log back on to calendar and reserve a time slot. To do so, select Go to the Online Scheduler under ‘My Quick Links’. Choose GeneMapper Remote in the ‘View schedule’ drop-down box. On the calendar, click on the time slot you want to reserve (all times are CST). In the ‘New Reservation’ window that appears, choose the starting and ending times of your session (please remember the time limit of 4 hours/day) and click Save to make your reservation. The scheduler will send you an e-mail confirming your reservation. Use the ‘My Reservations’ section on the control panel to view, edit or delete reservations.
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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/ http://www-app.igb.illinois.edu/biotech_schedule/].  Sessions are limited to 4 hours per customer per day.
  
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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.
  
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#Launch the Microsoft Remote Desktop Connection Client software. If you're running Windows XP, you will not need to download the client as it is already installed under Start > All Programs > Accessories > Communications. If you are running Windows 95, 98, 2000 or Mac OS, you will need to download the client software from http://www.microsoft.com/downloads. Search for “Remote Desktop Connection Client” and install the most recent version for your operating system.
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== Access ==
  
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*Please fill out the genemapper access form at [http://www.biotech.illinois.edu/form/biotech-genemapper-access-form http://www.biotech.illinois.edu/form/biotech-genemapper-access-form]
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*Once your account is activated you will be able to make reservations and login to Genemapper.
  
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#Launch the Remote Desktop Connection Client. In the computer field, enter 'genemapper.biotec.uiuc.edu'. Don’t click Connect until after completing Step 4.
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== Reservations ==
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    * For Windows, click on the arrow next to Options. It should expand to a window with several tabs.
 
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    * For MAC OS, go to RDC > Preferences. It should open a window with several tabs.
 
  
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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/ http://www-app.igb.illinois.edu/biotech_schedule/].
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*After signing in, click on the "Schedule" tab, "Bookings."
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*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.
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*Choose only one server: either "Genemapper - Remote 1" or "Genemapper - Remote 2.." '''Do not sign up for both at the same time.'''
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* When you double-click your choice of time, you can create a reservation. Choose your "Begin" time and your "End" time. Click "Create."
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*Click the "Sign Out" link at the top right of the page.
  
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#Set up your connection preferences.
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== Connecting ==
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    a. On the General (Windows) or Login (Mac) tab:
 
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        * Enter your username ‘XXXXXXX’ in the User Name field.
 
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        * Enter your password ‘XXXXXXX’ in the Password field.
 
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        * Enter ‘BIOTEC2’ in the Domain field.
 
  
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    b. On the Display tab:
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=== Genemapper Servers ===
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        * Choose ‘800 x 600’ for the size of the display to obtain the best performance.
 
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        * Choose 'Thousands' for the colors.  Millions will slow down the connection to the remote computer.
 
  
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    c. On the Local Resources (Windows) or Drives (Mac) tab, select a folder on your computer to be available for use on the Remote Desktop. We recommend that you create a unique folder for this purpose, so that other users on the Remote Desktop cannot access your personal files via the ‘My Computer’ or ‘Home’ folders. Use this folder to archive copies of your GeneMapper projects as you create them. 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!
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*genemapper1.biotech.illinois.edu
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*genemapper2.biotech.illinois.edu
  
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    d. For Windows only, click on the Performance tab and select your connection speed (i.e., dial-up, LAN, etc.).
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=== Connecting to Genemapper Computer ===
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Below are instructions on how to connect to the Genemapper servers.
  
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1.  Go to https://remote-gateway.igb.illinois.edu/guacamole/ and login with your IGB account username (netid or cbc_username) and your IGB password.
  
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#Click the Connect button. The GeneMapper window will open and you will see a Windows desktop. Launch the GeneMapper software and login using the same username and password that you used to set up the remote connection. Proceed with your analysis, and please remember to keep an eye on the time.
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2. There should be a "Genemapper" listed under 'All Connections'. Select the plus sign.
  
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3.  Then select genemapper1 or genemapper2.
  
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#At the end of your session, first exit out of the GeneMapper software and then disconnect from the remote server one of these two methods. 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.
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4. This opens a remote desktop session inside the web browser. Login again using your IGB account username and password.
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    * In the remote window, hit Control-Alt-Delete on your keyboard and choose the "Log Off" option in the window that appears (middle button on top row). Do not choose any of the other buttons because they will not log you off.
 
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    * In the remote window, go to START > Log Off.  Do not use the "Disconnect" option because it will not log you off.  
 
  
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Again, please let us know if you run into any problems. Happy analyzing!
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5.  Now you can go straight to the [[#Running_Genemapper_Software | Running_Genemapper_Software]] section.
  
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== Running Genemapper Software ==
  
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Remote GeneMapper Set-up with Windows 7
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*Double/click the shortcut on the desktop for the Genemapper software.
  
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#Launch the Remote Desktop Connection Client. Go to the Start menu then All Programs > Accessories > Remote Desktop Connection.
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*If your name is not available using the drop down arrow beside "User Name," type your netid or "[cbc_username]"
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In the computer field, enter 'genemapper.biotec.uiuc.edu'. Don’t click Connect until after completing Step 4.
 
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    * Click on the arrow next to Options. It should expand to a window with several tabs.
 
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#Set up your connection preferences.
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*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.
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    a. On the General tab:
 
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        * Enter your username ‘XXXXXXX’ in the User Name field.
 
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    b. On the Display tab:
 
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        * Choose ‘800 x 600’ for the size of the display to obtain the best performance.
 
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        * Choose 'High Color (16 bit)' for the colors.  If your computer seems really slow, you may want to change this to a lesser setting.   I have never done this part with Windows 7, so I do not know all the optimum settings.
 
  
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    c. On the Local Resources (Windows) or Drives (Mac) tab, select a folder on your computer to be available for use on the Remote Desktop. We recommend that you create a unique folder for this purpose, so that other users on the Remote Desktop cannot access your personal files via the ‘My Computer’ or ‘Home’ folders. Use this folder to archive copies of your GeneMapper projects as you create them. 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!  I could not find anywhere to choose a specific folder that I had created.  Maybe you have to choose a drive first.  You can also try choosing “Other supported Plug and Play devices and maybe save your data to flash drive.  Again, this is new to me, so you may have to adjust these settings later after you try using GeneMapper.
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*The Genemapper software will open.
  
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    d. Click on the Experience tab and select your connection speed (i.e., dial-up, LAN, etc.).  I chose LAN for use here on campus.
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*See [[#Tranferring_Data]] for optimum results in working with your data.
  
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*At the end of your session, first exit out of the GeneMapper software and then log off of the Genemapper computer. In the remote window, go to START > Sign out. Then, log out of https://remote-gateway.igb.illinois.edu/guacamole/.  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.
  
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#Click the Connect button. The GeneMapper window will open and you will see a Windows desktop. Launch the GeneMapper software and login using the same username and password that you used to set up the remote connection. Proceed with your analysis, and please remember to keep an eye on the time.
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== Transferring Data ==
  
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#At the end of your session, first exit out of the GeneMapper software and then disconnect from the remote server one of these two methods. 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.
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*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/ 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.
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    * In the remote window, hit Control-Alt-Delete on your keyboard and choose the "Log Off" option in the window that appears (middle button on top row). Do not choose any of the other buttons because they will not log you off.
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*Please remember to keep an eye on the time!
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    * In the remote window, go to START > Log Off.  Do not use the "Disconnect" option because it will not log you off.
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*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!'''

Latest revision as of 14:38, 24 July 2020


About[edit]

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[edit]

Reservations[edit]

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[edit]

Genemapper Servers[edit]

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

Connecting to Genemapper Computer[edit]

Below are instructions on how to connect to the Genemapper servers.

1. Go to https://remote-gateway.igb.illinois.edu/guacamole/ and login with your IGB account username (netid or cbc_username) and your IGB 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 again using your IGB account username and password.

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

Running Genemapper Software[edit]

  • 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. In the remote window, go to START > Sign out. Then, log out of https://remote-gateway.igb.illinois.edu/guacamole/. 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.

Transferring Data[edit]

  • 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!
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