Natural Science Software

Geneious Prime is a Bioinformatics software used for sequence analysis. It is currently used by both the Biology and Chemistry departments at Colby college.

We have 14 teaching and 5 research licenses for Geneious Prime. All licenses are floating licenses, meaning that while they can be used on multiple computers, only our set limit can be used at any concurrent time. Our research licenses are located on Sewall, and the classroom licenses on vwplic4.

Personal Research Use:

Geneious is already installed on classroom lab computers, but can be also installed on personal machines if the user has the correct server credentials and is on our Colby Network/VPN. If users need more information on how to get on our VPN, Ivanti, please visit here first to download it.  If users wish to install it on their personal machines, after obtaining the credentials from the HPC group, the easiest route is to directly download the software from the Biomatters website at https://www.geneious.com/download/. They have downloads available for Linux, Mac, and Windows machines. Please Note: We are currently only providing credentials to approved faculty and staff. If a student working under faculty would like to obtain credentials for their research, advising faculty should reach out to our group on their behalf.

If Faculty/Staff need to request credentials for their personal devices please reach us at [email protected].

If installing for the first time on a personal machine, after starting up the VPN or connecting to the Colby network, click on the Geneious Prime program to start the application. A pop-up window will request License details. You will want to enter the credentials under “License Server’ after setting the ‘Port’ to 28,001. The default is 27,001 so ensure that the port is correctly changed. Users will also have to enter in their email addresses for the benefit of having backups sent to their email account.

Once the correct License server credentials are entered, with the correct port, users should be able to successfully login. If for any reason the maximum amount of floating licenses are being used, users will receive this message:

In the event all seats are occupied. users may have to wait until another license frees up. If this becomes a consistent issue please contact the HPC team so that we may ensure they are being properly used by users.

For any issues with Geneious please submit a ticket request here.

MatLab is software that helps analyze data and draw out different models. Users interested in installing MatLab should first determine what the MatLab will be used for. There are generally two requests, Matlab for classroom use, and Matlab for research use. Our agreement with MathWorks (company that owns MatLab) is that MatLab for classroom use cannot be used in published research. Therefore, any requests for MatLab for research use must undergo a different method of installation.

Note: MatLab is the main software being used. There are sometimes requests for specific toolboxes (typical of research requests) that are essentially add-ons for the main software MatLab. They are an extra cost and do not come with the main software. The classroom version already comes with almost all of the toolboxes available at MatWorks.

Classroom Use: If a student requests Matlab for classroom use, they can install it from the ://Filer/Software. They must currently be enrolled in a classroom that is using MatLab to utilize this. There is a version for Mac and a separate version for Windows. There are also readme text files that have the activation code for the version being used, as well as any directions necessary for installation in that same folder. It is also available during non-classroom hours in Davis labs 101, 102, and 216. If students have difficulty installing it on their own machines they can also request access to our 3rd party virtual desktop Apporto if they do not already have access, and use the virtual desktop as an alternative.

If students are working in a research lab and need to utilize the software for research purposes, please visit our page here and to read the guide for Matlab research use.

If students have difficult installing Matlab on their personal devices please contact support at [email protected].

MatLab is software that helps analyze data and draw out different models. Users interested in installing MatLab should first determine what the MatLab will be used for. There are generally two requests, Matlab for classroom use, and Matlab for research use. Our agreement with MathWorks (company that owns MatLab) is that MatLab for classroom use cannot be used in published research. Therefore, any requests for MatLab for research use must undergo a different method of installation.

Note: MatLab is the main software being used. There are sometimes requests for specific toolboxes (typical of research requests) that are essentially add-ons for the main software MatLab. They are an extra cost and do not come with the main software. 

When there is a request to use MatLab for research there must first be a software request form filled out by clicking on the Software Request.

All research licenses cost money, as well as any needed toolboxes. Requesters must find funds prior to receiving a license. Typically, ITS can negotiate funding and will work with departments on covering the costs of the software depending on its use. When a software request is being filled out, please try to be as specific as possible about use of license, length needed, and designated computers it will need to be installed on. This will help determine the appropriate licensing funds.

After a software request has been made, the IT Budget Coordinator, will purchase the license from mathworks.com using the Colby account, as well as any toolboxes requested. There are currently 3 administrators able to view licenses Andrius Aukstuolis, Stephanie Drafahl, and Janna Hunnewell. Licenses under the administrative account can be viewed at https://www.mathworks.com/licensecenter/licenses.

Installing a Research License (students only): If a student is conducting research under advising faculty or staff, and require MATLAB on their personal machine, they must have faculty and/or staff submit a request on behalf of their student. Research licenses are under faculty and staff names, whereas only the owner of the license can grant permission to move it from one computer to another. If the faculty/staff wishes to purchase another license for their student they may do so through a software request. Please note as stated elsewhere, if a faculty/staff moves their own license from one computer to another for their student, there is a maximum limit of one license transfer per every 6 months. Licenses can only be used on one computer at a time.This is a Mathworks policy and non-negotiable.

Installing a Research License (faculty/staff only): Generally, a MatLab license can be installed by the requester using the information provided by the Budget Coordinator after purchase. Requesters will also be sent download permissions with an associated end user (requester). It’s typically an activation code, and depending on the type of OS, a license file might be required. Please note: A perpetual license purchase entitles the requester to updated MatLab versions so long as they pay the annual license fee. An annual license only entitles the user to whatever version they purchased at the time. Depending on the length of use of a MatLab license, Perpetual vs. Annual license needs will vary.

Transferring Research Licenses: Occasionally, there will be requests to move licenses from one computer to another. Sometimes, there is a computer upgrade whereas the old computer is no longer used. Other times, a faculty on sabbatical may agree to “lend” their license to another faculty for a short term. MatLab licenses are attached to designated machines. Currently, MathWorks only allows the transfer of a license 1x/6 month period. This limits the number of times a license can be transferred among computers. Is it important that this is understood to the person requesting the license transfer.

Mathworks requires that all active licenses first be deactivated from the current computer it is designated on. The instructions to deactivate a license on a computer are here https://www.mathworks.com/matlabcentral/answers/100663-how-do-i-deactivate-matlab After deactivation, activation on another computer is now possible. Download MatLab on the desired computer, and activate it from there. Please note again, that if an annual license was purchased only the version of MatLab at the time of purchase can be downloaded.

Any issues with license installation can be made into a ticket and referred to the Academic ITS – Research group. Please note: The AITS – Research Group is for assistance in research licenses only. Issues with downloading the classroom version should be referred to support.

Mestrenova is chemistry software from the Mestrelab Research company. It has several uses, one of which it can be implemented with NMR, LC/GC/MS, and other techniques. Typically, Mestrenova is used by Colby’s chemistry department throughout the year. The following is a guideline on how to obtain a copy of Mestrenova if requested by an instructor.

Please note: Mestrenova is licensed and verified on the Colby license server. For this reason, students or instructors using Mestrenova on their personal machines should ensure they are connected to the Colby network or VPN. If you are uncertain how to download and install our VPN Ivanti, please go here first: https://vpn.colby.edu/

Instructions for Download: 

Prior to installation of the software, it is best to download the license files (zip file). There are currently 7 separate license files compressed into a single .zip file. The best practice is to save the zip file on a desktop in which you can easily locate the files. This will later be used during the installation process, so it is important to note their exact location.

License Files (download zip file):

Colby College MestReNova

Please visit the Mnova download site and download the software. Please note that there are downloads for Windows, Mac, or Linux OS. Choose the one that adheres to your operating system, and install it.

After downloading the correct installer you will be led to the Setup Wizard. Click ‘Next” from here:

End-User License Agreement will come up. As suggested by the developer, please read and click ‘I accept the terms in the License Agreement’ followed by ‘Next’

For Installation settings users can decide if they want a desktop shortcut or not, as well as a start menu pin. Please select which ones preferred and click ‘Next’

On the next page Custom Setup should only be modified if users are experienced with disk usage and locations. Otherwise, users should use the default settings and click on ‘Next’

On the last installation step, users can click ‘Install’ when they’re ready to do so. This is followed up by a screen that will show you the status of installation complete. Once this step is completed click ‘Finish’. Please note that some computers may ask for permission to complete installation. This software is not a threat so long as it has been downloaded from the developer’s website (listed above) and should be granted permission.

Once installation is finished, depending on the OS used, the Mestrenova software may start up on it’s own, or may need to be opened again by the user. Opening the software again will not negatively impact the installation. Upon opening the software users should see this screen pop-up:

From this screen click ‘Install’ where a screen will pop up with your computer directories. From here select where on the computer the license files are and click ‘open.’ Please note here: License files can be selected altogether at once so that users do not have to add each individual one. Once the license files are installed users need to quit and restart Mestrenova for the license files to activate. Mestrenova should successfully install and be ready for use after this. If you have any questions please email [email protected] describing your issue with the software and OS you are using.