IPA Usage Instruction
Dear IPA User,
This document will provide you with information about the usage of the Ingenuity Pathway Analysis (IPA). We now have a license that is valid until July 2025. It is a - unlimited user, unlimited data sets but only 1 concurrency - license.
This means that only one user at a time is able to use IPA! The big advantage of this license is that your data sets stay within your own account and are not deleted after you used the software. That means you can work with your data and have breaks in between. For example, you can book IPA for 30 minutes to upload your data in the morning and another slot in the afternoon (or the next week, …) for when you do the analysis.
We have integrated the IPA software into the booking system of the Center for Molecular and Cellular Bioengineering (CMCB) to secure a fair usage and to manage the - only one user at a time - license principle. Before you are being able to book IPA, you need to register for the booking system and directly to the IPA software. Please plan some time in advance for your first usage of IPA as the registration process can take up to 3 working days. Once your registration is completed, you are able to book each IPA session via the booking system.
Pricing
We are offering two price models:
- If you rarely use the software, then it is possible to pay 60 Euro per hour.
- If you and your group are frequent users of IPA, then it is possible to pay 3,500 Euro for a full year per group. This is equivalent to a usage of 58 hours per year.
Both price models are valid for TU Dresden (TUD) internal funds. If you have other funds, please contact the CMCB Technology Platform (TP) accounting team at cmcb_tp_accounting(at)tu-dresden.de. Billing of fees (annual/hourly) will start as of 1st January 2023. Invoices for the annual fees for 2023 can be paid from October 2022 until March 2023. Please contact the CMCB TP accounting team with your accounting details and funding source.
Access to IPA
Step 1: Register for the booking system
Please contact the CMCB TP accounting team (cmcb_tp_accounting(at)tu-dresden.de), and ask for the “User Regulation” form of the CMCB TP. Fill out the form, and mark “Deep Sequencing” in “Cost coverage/approval of use for core facility/service unit” at the bottom of the form. Hand the signed form over to the CMCB TP accounting team (BIOTEC room 032, or via e-mail). An account for the booking system will be created for you with an ID and your provided e-mail address.
In addition, tell the CMCB TP accounting team to unlock your group for the usage of the IPA software.
Step 2: Create an IPA account
When you use IPA for the first time with this license, we need to register an IPA account for you. Please write an e-mail to the DRESDEN-concept Genome Center (DcGC, genomecenter(at)tu-dresden.de).
The subject of the mail has to be:
- Registration IPA Usage
and the content of the mail has to have:
- your e-mail address (it has to be an TUD e-mail address or an e-mail address from your institute, we cannot accept private e-mail addresses!)
- your name
- your group and institute (e.g., BIOTEC, CRTD, PoL, MPI, …).
We are going to create an IPA account, and login information will be sent to the provided e-mail address. Please follow the instructions in the mail. The provided e-mail address is the ID of your IPA account and this e-mail address will be used by the IPA staff to communicate with you.
Step 3: Book the IPA software with the booking system
You will find the IPA software under CRTD / CMCB – Dresden-concept Genome Center. The length of a standard booking slot is 30 minutes. We recommend to book not more then 3 hours in a row because of the fair usage principle.
Information about IPA
The whole principle for using IPA is the fair open usage of the software. Please stick to your booked time slots and book these slots in advance. Once your time slot is up, then log out of IPA. You will not lose your data because it belongs to your account.
IPA is either usable via installing a software or starting a client which needs an installed Java environment. You can download the software here. If you use a computer which is maintained by your local IT department, then please get in touch with them about installing the software. We cannot help you with software installation issues.
Mailing list
We also run an IPA mailing list (ipa(at)groups.tu-dresden.de). We will add your e-mail address to the mailing list when we register an IPA account for you. With this list, we will provide you with information like upcoming workshops. Furthermore, you can use this list to discuss issues about the software or make other users aware of features that you find interesting.
FAQ
I am overwhelmed with IPA’s functionality or I cannot find the function I’m looking for or I just need help with IPA.
We do not support issues related to the functionality of IPA. Please have a look at IPA’s Knowledge Base which lists many topics and you can get in touch with an IPA representative. Alternatively, you can write an e-mail to our local IPA mailing list (ipa(at)groups.tu-dresden.de) and ask for help.
I have to cancel my booking in the booking system.
Please write an email to CMCB TP accounting team (cmcb_tp_accounting(at)tu-dresden.de).
I cannot login because the license is already in use but I have a booked slot!
Login to the booking system. If someone booked a slot before your slot, then click on that slot and write this person an e-mail to the provided e-mail address and ask to log out. If this does not help, please write an e-mail to the mailing list (ipa(at)groups.tu-dresden.de) and/or the DcGC (genomecenter(at)tu-dresden.de). It may take a while for someone to reply. If there are cases where this is frequently happening, the admins of the software are able to terminate a live session and ongoing analyses will be lost, and it can escalate to a point where the admins revoke the access to IPA for that person.
I have funds which are not TUD funds but I want to use IPA.
Please contact the CMCB Technology Platform accounting team (cmcb_tp_accounting(at)tu-dresden.de).
Which e-mail address should I use for IPA?
You have to use an official e-mail address and not a private e-mail address. Ideally it should be an e-mail address from the TUD (and end on (at)tu-dresden.de) or from your institute (e.g. (at)mpi-cbg.de or (at)uniklinikum-dresden.de).
I have a computer which is maintained by the CMCB IT and want to install IPA.
For Windows, write an email to the IT (trouble(at)biotec.tu-dresden.de) and ask for an installation of the software.
For macOS, download software here, and change the application install location during the installation from /Applications/IPA to /Users/your-username-on-that-device/Applications/IPA
Get to know IPA
Here is a series of live hands-on training classes geared for new users:
IPA Training Videos
2-5 min training videos on specific advanced features in IPA:
- Regulator Effects Analysis: Provides insights into your data by integrating Upstream Regulator results with Downstream Effects results to create causal hypotheses that explain what may be occurring upstream to cause particular phenotypic or functional outcomes downstream.
- Molecule Activity Predictor: Simulate directional consequences of downstream molecules and the inferred activity upstream in the network or pathway.
- BioProfiler: Quickly profile a disease or phenotype by understanding its associated genes and compounds. Identify genes known to be causally relevant as potential targets or identify targets of toxicity, associated known drugs, biomarkers and pathways.
- Causal Network Analysis & Upstream Regulators: Identify upstream molecules that control the expression of the genes in your datasets.
- Pathway Activity Analysis: Determine if Canonical Pathways are increased or decreased based on your data. (Refer to the video on Molecule Activity Predictor)
- Comparison Analysis: Quickly visualize trends and similarities across analyses and datasets
- Isoform Content and Features for processing of RNA-Seq Data