Please note that registration for this course is now closed. You may still register by contacting us via E-Mail (This email address is being protected from spambots. You need JavaScript enabled to view it.) at this time, but we can not guarantee at the moment that you will be able to participate in this workshop. We will put you on our waiting list and will notify you if there should be more space available in a first come-first served order! The next planned workshop / tool training will take place at ILS 2021 (ils2021.org).

Please note that we currently have no automatic registration response E-Mail set up. You should receive a confirmation E-Mail from the organizers within 24 hours or on the next working day.
If you have any further questions, please contact the workshop organizers at This email address is being protected from spambots. You need JavaScript enabled to view it.

Educators:
Jacobo Miranda Ackerman, Fadi Al Machot, Nils Hoffmann (BioInfra.Prot / LIFS)

Date:
January 26th and 27th , 2021

Deadline for Workshop Registration:
January 19th, 2020

Location:
Online, virtual training.

Contents:
In the first part of the course (day 1), we will work through an example for targeted LC-MS lipidomics with LipidCreator and Skyline. In the second part of the course (day 1), we will apply PeakStrainer and LipidXplorer for filtering, identification and quantification of lipid signals from shotgun lipidomics. The course will consist of a short theory and background overview of the employed programs complemented by the application of the tools to provided data sets. The third part of this course (day 2) will work through a typical use-case of downstream data processing of shotgun lipidomics data following MS acquisition with LipidXplorer. We will inspect, check and normalize the data as well as calculate absolute quantities using internal class-specific standards with lxPostman. In part four (day 2), we will then perform a qualitative comparison of the lipidomes using the LUX Score lipidome homology.

The following times are in CET (GMT+1), Berlin time zone

Tuesday, January 26th
09:00 – 09:45 Welcome and Introduction
10:00 – 10:30 Targeted Lipidomics with LipidCreator and Skyline
10:30 – 13:00 LipidCreator and Skyline Exercises

Wednesday, January 27th
09:00 – 11:00 Shotgun Lipidomics with LipidXplorer
11:00 – 12:00 Quantification of Shotgun Lipidomics data with lxPostman
12:00 – 13:00 Lipidome comparison with LUX Score

Learning goals:
Participants will be able to understand and explain the shotgun MS and targeted LC-MS workflows for lipidomics. They will learn the fundamentals of the software tools used and how to choose parameters for them. They will learn to understand and interpret the results of each step of the pipeline.

Prerequisites:
Basic knowledge of lipidomics, analytical workflows in lipidomics and basic familiarity with web-based and desktop applications. Please note that you may need to install software on your computer to fully participate in all exercises which may require the proper rights. The workshop will be a mix of small lecture segments and hands-on exercises. The trainers will be available for questions and assistance during the workshop. We will use Zoom to host the workshop. To participate, please ensure that the Zoom client software is installed on your computer.

Keywords:
Lipidomics, Shotgun, Targeted, LC-MS

Tools:
PeakStrainer and LipidXplorer, LipidCreator, Skyline, lxPostman, LUX Score

Registration:

Registration is now closed.

Contact:
Nils Hoffmann This email address is being protected from spambots. You need JavaScript enabled to view it.

Instructions for Web Portal and Moodle access:
Please note that the workshop includes practical exercises, so to make the most of it, please make sure that your computer meets the following requirements:

• at least a 2-core CPU
• min. 4 - 8 GB RAM
• Windows 10
• up-to-date internet browser (Edge, Firefox, Chrome)
• ~ 2 GB of local disk space to download and install the necessary software and training data.

Some of the software used during the workshop will be available for use during the workshop via our web application portal.

About one week prior to the workshop, we will send registered and confirmed participants their access credentials.

Please go to the following page and log in with the provided credentials to activate your account:

1. https://apps.lifs.isas.de/login
2. Your user roles are available here:
   https://apps.lifs.isas.de/user
3. You should see the applications lifs-apps-webapp, lipidxplorer, luxscore, and shiny. If you click on any of them, you should see your assigned role for that application. In this case, this should be 'WSUSER' (LIFS workshop users) for the shiny application and 'USER' for the others.
4. If this is not the case, please let us know before the workshop!
5. You can then safely log-out again by clicking the red button on the top right, or by accessing the following page:
   https://apps.lifs.isas.de/login?logout

To access the Moodle for the workshop, please go to the following page to log in:

https://lifs.isas.de/moodle/login/

and click on the "LIFS App Portal" button on the right. You will then be redirected to the authentication server, where you can use the same username and password you already used for the application portal.

1. After entering your username and password, our Moodle will send an e-mail to your registered e-mail account.
2. Please check your spam folder, too. The e-mail will have the subject line "LIFS Moodle E-Learning Platform: account confirmation".
3. Please either click on the link contained in the e-mail or copy and paste it manually into your browser.
4. After one final request to accept our privacy policy, you should be logged in to our Moodle.

Additional Software Installation Required:

This workshop contains parts that require local software to be installed on the participant's computer.

Skyline and LipidCreator

1. Go to this homepage https://skyline.ms/wiki/home/software/Skyline/page.view?name=SkylineInstall_64_20-2 to download Skyline, if you do not have it installed yet.
2. Install it, then start Skyline and create a new document.
3. Go to "Tools", "Tool Store...", select "LipidCreator" and click "Install".
4. Wait until the installation has finished.
5. Click on "Tools" and you should see a "LipidCreator" menu item to start LipidCreator.

LipidXplorer

1. Go to this link to download LipidXplorer: https://lifs.isas.de/releases/lipidxplorer/1.2.8.1/LipidXplorer-1.2.8.1.zip
2. If you just place the zip in a folder, unpack / unzip / extract it, then open the extracted folder.
3. You should find LipidXplorer.exe in the folder.
4. Double click LipidXplorer.exe to start it.
5. Potentially, Windows could ask you to allow execution of the program.

All other tools necessary for the workshop will be available as web applications.

This workshop is kindly supported by the German Network for Bioinformatics Infrastructure (de.NBI) and Elixir Germany:

As part of this year's online, virtual joint European Lipidomics Meeting and Lipidomics Forum 2020 LIFS offers a one day online workshop on Bioinformatics for Lipidomics.

Please note that this course has already exceeded its planned capacity of 40 participants. You may still register by contacting us via E-Mail (This email address is being protected from spambots. You need JavaScript enabled to view it.) at this time, but we can not guarantee at the moment that you will be able to participate in this workshop. We will put you on our waiting list and will notify you if there should be more space available in a first come-first served order! Depending on further demand, we may offer an additional workshop later this year or early next year.

Please note that we currently have no automatic registration response E-Mail set up. You should receive a confirmation E-Mail from the organizers within 24 hours or on the next working day.
If you have any further questions, please contact the workshop organizers at This email address is being protected from spambots. You need JavaScript enabled to view it.

Educators:
Jacobo Miranda Ackerman, Fadi Al Machot, Nils Hoffmann (BioInfra.Prot / LIFS)

Date:
October 1st, 2020
Deadline for Workshop Registration:
September 25th, 2020

Location:
Online, virtual workshop as part of the joint European Lipidomics Meeting & Lipidomics Forum 2020.

Contents:
In the first part of the course, we will work through an example for targeted LC-MS lipidomics with LipidCreator and Skyline. In the second part of the course, we will apply PeakStrainer and LipidXplorer for filtering, identification and quantification of lipid signals from shotgun lipidomics. The course will consist of a short theory and background overview of the employed programs complemented by the application of the tools to provided data sets. The third part of this course will work through a typical use-case of downstream data processing of shotgun lipidomics data following MS acquisition with LipidXplorer. We will inspect, check and normalize the data as well as calculate absolute quantities using internal class-specific standards with lxPostman. We will then perform a qualitative comparison of the lipidomes using the LUX Score lipidome homology.

09:00 – 09:30 Welcome and Introduction
09:30 – 12:00 Targeted Lipidomics with LipidCreator and Skyline
12:00 – 13:00 Break
13:00 – 15:00 Shotgun Lipidomics with PeakStrainer and LipidXplorer
15:00 – 16:00 Downstream processing with lxPostman
16:00 - 17:00 Lipidome comparison with LUX Score

Learning goals:
Participants will be able to understand and explain the shotgun MS and targeted LC-MS workflows for lipidomics. They will learn the fundamentals of the software tools used and how to choose parameters for them. They will learn to understand and interpret the results of each step of the pipeline.

Prerequisites:
Basic knowledge of lipidomics, analytical workflows in lipidomics and basic familiarity with web-based and desktop applications. Please note that you may need to install software on your computer to fully participate in all exercises which may require the proper rights. The workshop will be a mix of small lecture segments and hands-on exercises. The trainers will be available for questions and assistance during the workshop. We will use Zoom to host the workshop. To participate, please ensure that the Zoom client software is installed on your computer.

Keywords:
Lipidomics, Shotgun, Targeted, LC-MS

Tools:
PeakStrainer and LipidXplorer, LipidCreator, Skyline, lxPostman, LUX Score

Registration:

Registration is now closed.

Contact:
Nils Hoffmann This email address is being protected from spambots. You need JavaScript enabled to view it.

Instructions for Web Portal and Moodle access:
Please note that the workshop includes practical exercises, so to make the most of it, please make sure that your computer meets the following requirements:

• at least a 2-core CPU
• min. 4 - 8 GB RAM
• Windows 10
• up-to-date internet browser (Edge, Firefox, Chrome)
• ~ 2 GB of local disk space to download and install the necessary software and training data.

Some of the software used during the workshop will be available for use during the workshop via our web application portal.

Please go to the following page and log in with the provided credentials to activate your account:

1. https://apps.lifs.isas.de/login
2. Your user roles are available here:
   https://apps.lifs.isas.de/user
3. You should see the applications lifs-apps-webapp, lipidxplorer, luxscore, and shiny. If you click on any of them, you should see your assigned role for that application. In this case, this should be 'WSUSER' (LIFS workshop users) for the shiny application and 'USER' for the others.
4. If this is not the case, please let us know before the workshop!
5. You can then safely log-out again by clicking the red button on the top right, or by accessing the following page:
   https://apps.lifs.isas.de/login?logout

To access the Moodle for the workshop, please go to the following page to log in:

https://lifs.isas.de/moodle/login/

and click on the "LIFS App Portal" button on the right. You will then be redirected to the authentication server, where you can use the same username and password you already used for the application portal.

1. After entering your username and password, our Moodle will send an e-mail to your registered e-mail account.
2. Please check your spam folder, too. The e-mail will have the subject line "LIFS Moodle E-Learning Platform: account confirmation".
3. Please either click on the link contained in the e-mail or copy and paste it manually into your browser.
4. After one final request to accept our privacy policy, you should be logged in to our Moodle.

Additional Software Installation Required:

This workshop contains parts that require local software to be installed on the participant's computer.

Skyline and LipidCreator

1. Go to this homepage https://skyline.ms/wiki/home/software/Skyline/page.view?name=SkylineInstall_64_20-1 to download Skyline, if you do not have it installed yet.
2. Install it, then start Skyline and create a new document.
3. Go to "Tools", "Tool Store...", select "LipidCreator" and click "Install".
4. Wait until the installation has finished.
5. Click on "Tools" and you should see a "LipidCreator" menu item to start LipidCreator.

LipidXplorer

1. Go to this link to download LipidXplorer: https://lifs.isas.de/releases/lipidxplorer/1.2.8.1/LipidXplorer-1.2.8.1.zip
2. If you just place the zip in a folder, unpack / unzip / extract it, then open the extracted folder.
3. You should find LipidXplorer.exe in the folder.
4. Double click LipidXplorer.exe to start it.
5. Potentially, Windows could ask you to allow execution of the program.

All other tools necessary for the workshop will be available as web applications.

This workshop is kindly supported by the German Network for Bioinformatics Infrastructure (de.NBI) and Elixir Germany:

LIFS Training Workshops @ Lipidomics Forum 2019

Before this year's Lipidomics Forum 2019 in Borstel, Germany kicks off on the evening of Sunday, November 10th, 2019, LIFS will host two lipidomics tool and workflow workshops. Based on the participant surveys of previous trainings, we will offer two separate courses this year to allow for more hands-on time with the tools and data.

Please go to the Lipidomics Forum registration to sign up for one of the courses (they will be taught in parallel).

Workshop 1 - Lipidomics MS Data processing, identification & quantification

"What is it and how much?"

10:00 - 10:45 Common Introduction
10:45 - 12:30 LipidXplorer Shotgun Lipidomics
12:30 - 13:30 Lunch break
13:30 - 16:30 LipidCreator & Skyline Targeted LC-MS lipidomics

Educators:
Jacobo Miranda Ackermann, Nils Hoffmann (BioInfra.Prot / LIFS)

Date:
November 10th, 2019

Location:
Forschungszentrum Borstel, Borstel, Germany (as part of Lipidomics Forum 2019)

Contents:
In this course, we will work through a typical use-case for bioinformatics processing lipidomics data following MS acquisition. The first part of the course will start with PeakStrainer and LipidXplorer for filtering, identification and quantification of lipid signals from shotgun lipidomics. The second part of the course will work through an example for targeted LC-MS lipidomics with LipidCreator and Skyline. The course will consist of a short theory and background overview of the employed programs complemented by the application of the tools to a provided data set.
 
Learning goals:
Participants will be able to understand and explain the shotgun MS and targeted LC-MS workflows for lipidomics. They will learn the fundamentals of the software tools used and how to choose parameters for them. They will learn to understand and interpret the results of each step of the pipeline.

Prerequisites:
Basic knowledge of lipidomics, analytical workflows in lipidomics and basic familiarity with web-based and desktop applications. Participants are required to bring their own laptop in order to work on the hands-on exercises.

Keywords:
Lipidomics, Shotgun, Targeted, LC-MS

Tools:
PeakStrainer and LipidXplorer, LipidCreator and Skyline.

Workshop 2 - Statistical analysis & qualitative and quantitative comparison of lipidomics data

"How do I compare? Fancy graphics & convincing plots"

10:00 - 10:45 Common Introduction
10:45 - 12:30 R Scripting for LipidXplorer data quantification
          Quantitative lipidome comparison wiht ClovR
12:30 - 13:30 Lunch break
13:30 - 16:30 Qualitative lipidome with LUX Score
          Machine learning, clustering and classification for lipidomics data

Educators:
Fadi al Machot, Nils Hoffmann (BioInfra.Prot / LIFS)

Date:
November 10th, 2019

Location:
Forschungszentrum Borstel, Borstel, Germany (as part of Lipidomics Forum 2019)

Contents:
In this course, we will work through a typical use-case of downstream data processing of shotgun lipidomics data following MS acquisition with LipidXplorer. We will  absolute quantification against internal class-specific standards comparison of the lipidomes using the LUX Score lipidome homology, before finally comparing and visualizing our quantitative lipidome results with ClovR. The course will consist of a short theory and background overview of the employed programs complemented by the application of the tools to provided data sets.
 
Learning goals:
Participants will be able to understand and explain the shotgun lipidomics data analysis workflow. They will learn the fundamentals of the software tools used and how to choose parameters for them. They will learn to understand and interpret the results of each step of the pipeline.

Prerequisites:
Basic knowledge of lipidomics, analytical workflows in lipidomics and basic familiarity with web-based applications. Basic knowledge of R and RStudio is a plus to understand the quantitation workflow. Participants are required to bring their own laptop in order to work on the hands-on exercises.

Keywords:
Lipidomics, Statistical Analysis, Visualization

Tools:
R and RStudio, LUX Score, ClovR.

Contact

If you have any questions about the training workshops, please use our Service & Support form.

Acknowlegements

We thank de.NBI - the German Network for Bioinformatics Infrastructure and Elixir for their support.