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Topics - Jan Stanstrup

1
Other / Access NIST library from R or similar
Does anyone know if there is a way to direct access to the data in the NIST library? I would like to automate some things in R but the NIST library seems to be in some binary format.
Have someone done something similar?
Any hints?
2
Join a free online course in EdX

The first MOOC of its kind, this course is an introduction to metabolomics principles and their applications in various fields of life sciences.

We will provide a summary of all steps in metabolomics research; from experimental design, sample preparation, analytical procedures, to data analysis. The course also provides case studies of various kinds of research samples to attract students that are not familiar with metabolomics, providing them enough explanation to utilize metabolomics technology for their respective research fields.

Several examples of metabolomics applications will be introduced throughout the lectures. These include examples within food science and technology, metabolic engineering, basic biology, introduction to imaging mass spectrometry, and application in medical science.

No previous knowledge on metabolomics is needed but we recommend that students have an undergraduate-level understanding of Biochemistry, Analytical Chemistry, and Biostatistics, and that they learn about basic principles of multivariable analysis prior to taking this course.

To register please access this link https://www.edx.org/course/metabolomics-life-sciences-osakaux-metab101x#!
3
Tools / post-acquisition centroiding of Waters data
Hi,

I was wondering if anyone knows a way to get good centroiding of Waters data that was recorded in profile mode?
In MassLynx you can centroid a single spectrum and it looks like this as an example:



That seems reasonable by eye.
I tried then using the centroiding in msconvert (Proteowizard). Here is the result:




What it has done is not finding the center of the peak but has chosen the top scan for the m/z. This is not very accurate and is in this case a difference of 15 ppm.

So my question is if someone knows a better way to centroid data that was already acquired?
Msconvert can use vendor algorithms for centroiding for a lot of formats but apparently it is not available for waters data.
4
The last webinar "Machine learning powered metabolomic network analysis" by Dr. Dmitry Grapov is now online.

http://metabolomicssociety.org/resources/videos/88-videos/258-2017-emn-webinars-public

6
http://www.moviss.eu/

When: Sept 25-27 2017
Where: Vorau, Austria
To register and for more information, go to www.MOVISS.eu, and follow us on Twitter @MOVISSmeet

More information:
We would like to invite you to Bio&Data, the first workshop of the newly established MOVISS - "Mountain Village Science Series" taking place in Vorau, Austria (Sep 20-23, 2017). MOVISS Bio&Data is different to the usual conferences. It is rather constructed as a small, problem-driven meeting, full of discussions and questions about how to deal with metabolomics data reasonably. In this way, we hope to constructively engage some of the greatest minds collaboratively in solving some of the challenges of the metabolomics and bioinformatics community.

Four sessions are planned, each devoted to a separate step of the metabolomics process; Design of Experiments, Analytical Analysis, Data Processing and Statistical Analysis in the biosciences will all be discussed including your data if you bring them for discussions.

We plan a summary of this discussion will be produced as a paper for publication to share within the wider metabolomics community. Finally, you can continue with the R Summer School from September 25 - 27, 2017 in Vorau!
7
Conferences and seminars / Metabomeeting 2017
The 10th Metabomeeting will be held at the University of Birmingham in the UK on the 11-13th December 2017.

The deadline for oral presentation abstracts is 15th July 2017
The deadline for poster abstracts is 1st October 2017.


The meeting agenda will be available on the conference web-site and will include sessions on some or all of the following:
  • Applied Metabolomics 
  • Drug Discovery and Development
  • Human Disease and Nutrition 
  • Microbial, Invertebrate and Environmental applications 
  • Plants 
  • Data Analysis and Integration with Systems Biology 
  • Metabolite Identification 
  • Data Modelling and Data Interpretation 
  • Workflows and Computational Metabolomics 
  • Analytical Approaches and Developments 
  • Lipidomics
  • Stable Isotope Metabolomics and imaging
  • Lipidomics
  • Method standardisation 
  • Early career scientists

Link: http://metabomeeting2017.thempf.org/
8
Announcements / Metabolomics Society conference 2017

Join your Metabolomics peers in 2017!

We are delighted to announce that Early bird registration is open for Metabolomics 2017 - the 13th Annual Conference of the Metabolomics Society. We look forward to seeing you in Brisbane! Please visit the new website for more information and take advantage of the early-bird pricing.

Website:
Metabolomics 2017

Hosted by: The Metabolomics Society
Where: Brisbane, Queensland, Australia
When: June 26-29, 2017

Abstract submission information will be published within the next month. We look forward to seeing your latest findings!

The Society has obtained a group block of hotel rooms, visit the Hotel page of the website to view several different options. You are encouraged to book your hotel accommodation as soon as possible, since June is a very busy time inBrisbane.

Happy New Year!
The Metabolomics 2017 Planning Team
9
The EMN's next webinar is next week.

Click here to learn more about this latest webinar by Dr. Stephan Hann.

Please register for "How well do I quantify? Concepts for method validation and evaluation of measurement uncertainty in metabolomics" to be held on February 01st, 2017 14:00 UTC/14:00 GMT at: 

https://attendee.gotowebinar.com/register/61200296851992065
10
Other / Introduction to Nutritional Metabolomics
At time of writing there are 6 seats left. Don't miss out!


Content
The course will provide an introduction to the LC-MS based nutritional metabolomics studies, aiming to cover key steps such as study design, sample collection and analysis, data handling methodologies and metabolite identification.

The students will go through common steps in a typical metabolomics study. Therefore, the major focus will be application of various free or commercial tools for data preprocessing, data analysis, and metabolite identification with computer based hands-on training using example datasets that will be provided to the students.

The course will finalize by presentations of reports generated by the students based on a case study.

SCIENCE, NordFOOD and NUGO homepages only. A limit of 16 participants has been set this year.


Learning outcome
The aim of this course is to introduce the students to all phases in a nutritional metabolomics study and to train the student in the use of available tools for data handling. Both targeted and untargeted LC-MS methodologies will be thought, yet major focus of the course is untargeted LC-MS based metabolomics.

After completing the course the students should be able to:

• Evaluate the effect of study design on data handling and interpretation of final outcome
• Suggest the sample type to analyze for a specific research question and propose the relevant sample collection and preparation procedure 
• Understand the basic principles of LC-MS technology
• Carry out data preprocessing on using freely available tools such as MZmine 
• Perform univariate and multivariate analysis on R/MATLAB 
• Interpret the MS/MS spectra by utilizing available tools (e.g. CAMERA, MetFusion, MetFrag) and databases (e.g. HMDB, MassBank, MZCloud)


Teaching and learning methods
Lectures, hands-on exercises, group discussions.


Lecturers
• Lars O. Dragsted
• Gözde Gürdeniz
• Jan Stanstrup
• Rastislav Monosik
• Mads Vendelbo Lind 


Link: https://phdcourses.ku.dk/DetailKursus.aspx?id=102145&sitepath=NAT
11
The EMN's next webinar is tomorrow: Smarter ways to clean LC-MS data: Use of QCs for between- and within-batch signal correction.

Click here to learn more about this latest webinar by Dr. Carl Brunius.

Please register for "Smarter ways to clean LC-MS data: Use of QCs for between- and within-batch signal correction" to be held on November 17th, 2016 11:00 UTC/12:00 BST at: 

https://attendee.gotowebinar.com/register/5575746988123613187

After registering, you will receive a confirmation email with information about joining the webinar.

Brought to you by the EMN of the Metabolomics Society
12
RMassBank / parser for massbank record --> R (list)
RMassBank first creates a list structure for the info that goes in the RMassBank record, but is there a way to go the other way?
--> A parser to read the RMassBank txt files into an R friendly structure.
13
In the Systems Medicine research group (metabolomics and lipidomics) at Steno Diabetes Center (Denmark) we are looking for a new PI to lead the group. Please help spread the word to possible candidates.

Application deadline: November 1st.

Please check out the position here: http://www.novonordisk.com/careers/see-list-of-all-available-jobs.42515BR.External.html?cid=LI-42515BR
14
Site related / Logo needed for @MetSoc-Forums
It was kindly pointed out by @egonwillighagen that we need a logo for the @MetSoc-Forums twitter account.
Any takers?
15
Announcements / Announcing new forum
Dear members of the Metabolomics Society and users of the metabolomics forums,

The Website and Communications Committee, of the Metabolomics Society is excited to announce that we have now merged and updated the previous version of the metabolomics-forum.com and the Metabolomics Society's forums (previously interest-groups.metabolomicssociety.org).
We hope that this new forum will re-ignite vibrant discussions on all things metabolomics. We have packed the new forum with new features to inspire just that. Please read below in the next post, if you want to know more about some of the new features. Please give us feedback and comments for improvement, all suggestion are welcomed. Please use the site related forum for suggestions and bug reports.

Old forum profiles
Because we merged the two old forums into a whole new forum there might have been some changes to your old user account. Following changes has been implemented:
we merged some accounts with the same name (or user ID) to avoid duplicate accounts.
In all cases the password from metabolomics-forum.com was used for the new account.
Please check your previous usernames in the user list and let me know if your accounts were not merged.

To avoid carrying over a lot of spam accounts, we have deleted all accounts with zero posts. Please feel free to create a new account if yours was deleted, our apologies for that there was no easy way to "separate the wheat from the chaff".
For users moving over from the Metabolomics Society forum, you might have to reset your password to be able to login.