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1
Birmingham Metabolomics Training Centre / Quality Assurance and Quality Control in Metabolomics, Mar 2021

Quality Assurance and Quality Control in Metabolomics

Start Date: Monday 08 March 2021
End Date: Friday 26 March 2021

Location: Online (FutureLearn)



Course Overview
The application of quality assurance and quality control in the metabolomics field is vital to ensure the collection of high quality data. In this course you will explore the importance of quality assurance and quality control in both untargeted and targeted metabolomics studies. We will explain the difference between quality control and quality assurance and how to apply in your studies and laboratories. You will evaluate the types of quality control samples that can be applied in metabolomics, what is the most appropriate quality control sample to use in your research, and how to apply the data in your quality assurance procedure to produce robust and reproducible data.

The materials in this course are delivered via the FutureLearn platform over a three week period, with an estimated learning time of four hours per week. Each week you will work through a number of steps to complete the learning material. A step may include a short video, an article, an exercise with step-by-step instructions, a discussion to interact with your peer and a selection of quizzes, tests and polls to self-assess your own learning. All of the course material is uploaded to the FutureLearn platform so that you can complete the steps at a convenient time for you.

We (the educators) support your learning via social discussions where you will be able post questions and comments to the team of educators and the other learners on the course throughout the three weeks.

In the final week of the course we will record a summary video where we will respond to questions posted by you during the course.

If you do not have time to complete the course during the 3-week period you will retain access to the course material to revisit, as you are able.

Topics Covered
  • What are quality assurance and quality control and how do they differ
  • What is the importance of quality assurance in metabolomics
  • The types of quality assurance and quality control in untargeted and targeted metabolomics
  • The importance of quality control samples
  • The types of quality control samples applied in untargeted and targeted metabolomics
  • Preparation of quality control samples in untargeted and targeted metabolomics
  • Analytical studies including untargeted and targeted metabolomics
  • Processing data in untargeted and targeted metabolomics
  • Recommended quality assurance procedures in untargeted and targeted metabolomics
  • Reporting quality assurance procedures in untargeted and targeted metabolomics

Level
This course would be ideally suited to first year MSc / PhD students or scientists who are in the early stages of performing metabolomics studies. No previous knowledge of quality assurance and quality control in metabolomics is assumed, but a basic understanding of the metabolome, and the analytical techniques applied in the metabolomics field would be beneficial. A pre-course recommended reading list is provided.

If you would like to discuss if your level of knowledge is suitable for the course please contact us at bmtc@contacts.bham.ac.uk

Cost
Early-bird Registration: £180 (Rate expires: 07 February 2021)
Standard Registration: £200 (Rate expires: 26 March 2021)

Course link & Registration
https://www.birmingham.ac.uk/facilities/metabolomics-training-centre/courses/2021/quality-control-and-quality-assurance-in-metabolomics.aspx
2
Birmingham Metabolomics Training Centre / Metabolomics Data Processing and Data Analysis, Feb 2021
Metabolomics Data Processing and Data Analysis



Start Date: Monday 01 February 2021
End Date: Friday 26 February 2021

Location: Online (FutureLearn)

Course Overview
This online course explores the tools and approaches that are used to process and analyse metabolomics data. You will investigate the challenges that are typically encountered in the analysis of metabolomics data, and provide solutions to overcome these problems.

The materials in this course are delivered via the FutureLearn platform over a four week period, with an estimated learning time of four hours per week. Each week you will work through a number of steps to complete the learning material. A step may include a short video, an article, an exercise with step-by-step instructions, a test or a discussion to interact with your peer or the educators. All of the course material is uploaded to the FutureLearn platform so that you can complete the steps at a convenient time for you.

We (the educators) support your learning via social discussions where you will be able post questions and comments to the team of educators and the other learners on the course throughout the 4 weeks.

In the final week of the course there is a live question and answer session with the entire team of educators. You will be provided with information to join the question and answer session via the FutureLearn platform and you can post questions in advance. The question and answer session will be recorded and a video uploaded to the FutureLearn platform.

If you do not have time to complete the course during the 4-week period you will retain access to the course material to revisit, as you are able.

Topics Covered
  • An introduction to metabolomics
  • An overview of the untargeted metabolomics workflow
  • The influence of experimental design and data acquisition on data analysis and data quality
  • Processing of NMR data
  • Processing direct infusion mass spectrometry data
  • Processing liquid chromatography-mass spectrometry data
  • Reporting standards and data repositories
  • Data analysis, detecting outliers and drift, and pre-treatment methods
  • Univariate data analysis
  • Multivariate data analysis (including unsupervised and supervised approaches)
  • The importance of statistical validation of results
  • Computational approaches for metabolite identification and translation of results into biological knowledge
  • What are the future challenges for data processing and analysis in metabolomics

Software used during the course
  • Galaxy to process direct infusion mass spectrometry data
  • XCMS online to process liquid chromatography - mass spectrometry data
  • MetaboAnalyst in the univariate and multivariate data analysis exercises
  • Metabolite annotation using PUTMEDID_ID operating in the Taverna workflow environment

Level
The course would be ideally suited to MSc / PhD students or scientists who are in the early stages of analysing metabolomics data. No previous knowledge of the data processing and statistical analysis approaches is assumed, but a basic understanding of the metabolome, and the analytical techniques applied in the metabolomics field would be beneficial. A pre-course recommended reading list will be provided.

Cost
Early-bird Registration: £230 (Rate expires: 17 January 2021)
Standard Registration: £250 (Rate expires: 26 February 2021)

Course link & Registration
https://www.birmingham.ac.uk/facilities/metabolomics-training-centre/courses/2021/metabolomics-data-processing-and-data-analysis-february-2021.aspx
3
Job opportunities / PhD position in Metabolomics : BBSRC iCASE with Unilever
Project Description

Ensuring chemical safety through toxicity studies in Daphnia using state-of-the-art molecular, imaging and modelling approaches

This exciting 4-year BBSRC iCASE PhD opportunity bridges the University of Birmingham’s (*) metabolomics team and Unilever’s Safety and Environmental Assurance Centre (SEAC), both having state-of-the-art facilities and renowned research programmes, thereby creating an excellent environment for this challenging yet impactful research project.

* Winner of ‘University of the Year for Graduate Employment’, The Times and The Sunday Times Good University Guide 2015-16; 91% of our postgraduate researchers from the School of Biosciences were in work and/or further study six months after graduation.

Project Description

A revolution is now occurring in bioscience, driven by the availability of highly sensitive molecular technologies that can generate ‘big data’ to drive new understandings of molecular function. These technologies can help to create quantitative models of organism function. Of major importance, and often overlooked, is modelling the effect that organisms can have on the stressor (to complement the more-often studied effect the stressor can have on the organism) – representing a critical element of exposure science. Understanding how species deal with increasing chemical stressors (both from natural sources and/or anthropogenic-activities) will deeply influence the way we manage the potential risk of these stressors.

In a rapidly changing world with ecosystems under unprecedented pressures, leading to biodiversity loss at a rate never observed before, bio-analytical approaches used in tandem with computational modelling are key to deal with the problem. In an attempt to mitigate this pressure, there is an impelling need to understand the most sensitive physiological properties of organisms (and their underlying molecular mechanisms). To achieve this prognostically within a safety assessment framework, i.e. to characterize the stressor before it’s allowed to enter the environment, the decision-making requires quantitative exposure and effect models, as highlighted by the recent publication of an “opinion on the state-of-the-art of Toxicokinetic/Toxicodynamic effect models for regulatory risk assessment” by EFSA. This is where new, advanced, bio-analytical and molecular technologies can have a key role in the way we face this challenge, which we will explore within this PhD.

How to Apply

To apply for this position, please visit the FindAPhD site: https://www.findaphd.com/phds/project/ensuring-chemical-safety-through-toxicity-studies-in-daphnia-using-state-of-the-art-molecular-imaging-and-modelling-approaches/?p105864

Please also email Professor Mark Viant to let him know of your interest in this role.
4
Job opportunities / Postdoctoral Fellow in Mass Spectrometry-based Metabolomics
Post: Postdoctoral Fellow in Mass Spectrometry-based Metabolomics
Department: IU Bloomington Public & Environmental Affairs

Full text: https://indiana.peopleadmin.com/postings/6871

Position Summary:
We are recruiting a postdoctoral fellow in Mass Spectrometry-based Metabolomics at Indiana University Bloomington to participate in an exciting, new collaborative project called PhyloTox, which seeks to identify the evolutionary origins of molecular toxicity pathways. Using transcriptomics and metabolomics data collected from a group of model species/cells exposed to a carefully selected suite of chemicals, biological insights will be drawn from the perturbation of entire genetic and biochemical networks via chemical ablation. The ultimate goal of the project is to develop a novel precision environmental health program to help solve the enormous environmental health crisis caused by environmental pollution.

For this position, we seek a postdoctoral fellow in Mass Spectrometry Metabolomics to focus on the application of metabolic phenotyping across a six model organisms/cell lines, applying primarily non-targeted LC-MS strategies. The post-holder will perform sample preparation applying manual and robotic approaches, LC-MS instrument maintenance and operation to acquire highly reproducible data in a high-throughput laboratory, and metabolite identification. They will contribute to study design and analytical method development in cutting edge, biomedical computational and statistical analysis.

The project involves working with several PIs and laboratories and, thus, collaborative skills and results-oriented project management are required. The position is localized at Indiana University Bloomington in the School of Public and Environmental Affairs, Department of Chemistry, Department of Environmental Health, and Department of Intelligent Systems Engineering. The position also includes a unique training opportunity under the guidance of Prof Mark Viant in the world class metabolomics facility of the University of Birmingham, UK (https://www.birmingham.ac.uk/staff/profiles/biosciences/viant-mark.aspx). This position will either be assigned to the Department of Chemistry or the School of Public and Environmental Affairs, whichever is the best fit for the successful candidate.

Questions regarding the position or application process can be directed to: Drs. Joseph Shaw (joeshaw@indiana.edu) or Stephen Jacobson (jacobson@indiana.edu).

To apply: Interested candidates should review the application requirements and submit their application online: https://indiana.peopleadmin.com/. The application should consist of a cover letter stating your accomplishments and interest in the project’s research, curriculum vitae, and letters of support from at least two references. Review of applications will begin immediately and continue until the position is filled. Applications received by November 15, 2018 will receive full consideration.
5
Job opportunities / Postdoctoral Fellow in Mass Spectrometry-based Metabolomics
Post: Postdoctoral Fellow in Mass Spectrometry-based Metabolomics
Department: IU Bloomington Public & Environmental Affairs

Full text: https://indiana.peopleadmin.com/postings/6871

Position Summary:
We are recruiting a postdoctoral fellow in Mass Spectrometry-based Metabolomics at Indiana University Bloomington to participate in an exciting, new collaborative project called PhyloTox, which seeks to identify the evolutionary origins of molecular toxicity pathways. Using transcriptomics and metabolomics data collected from a group of model species/cells exposed to a carefully selected suite of chemicals, biological insights will be drawn from the perturbation of entire genetic and biochemical networks via chemical ablation. The ultimate goal of the project is to develop a novel precision environmental health program to help solve the enormous environmental health crisis caused by environmental pollution.

For this position, we seek a postdoctoral fellow in Mass Spectrometry Metabolomics to focus on the application of metabolic phenotyping across a six model organisms/cell lines, applying primarily non-targeted LC-MS strategies. The post-holder will perform sample preparation applying manual and robotic approaches, LC-MS instrument maintenance and operation to acquire highly reproducible data in a high-throughput laboratory, and metabolite identification. They will contribute to study design and analytical method development in cutting edge, biomedical computational and statistical analysis.

The project involves working with several PIs and laboratories and, thus, collaborative skills and results-oriented project management are required. The position is localized at Indiana University Bloomington in the School of Public and Environmental Affairs, Department of Chemistry, Department of Environmental Health, and Department of Intelligent Systems Engineering. The position also includes a unique training opportunity under the guidance of Prof Mark Viant in the world class metabolomics facility of the University of Birmingham, UK (https://www.birmingham.ac.uk/staff/profiles/biosciences/viant-mark.aspx). This position will either be assigned to the Department of Chemistry or the School of Public and Environmental Affairs, whichever is the best fit for the successful candidate.

Questions regarding the position or application process can be directed to: Drs. Joseph Shaw (joeshaw@indiana.edu) or Stephen Jacobson (jacobson@indiana.edu).

To apply: Interested candidates should review the application requirements and submit their application online: https://indiana.peopleadmin.com/. The application should consist of a cover letter stating your accomplishments and interest in the project’s research, curriculum vitae, and letters of support from at least two references. Review of applications will begin immediately and continue until the position is filled. Applications received by November 15, 2018 will receive full consideration.
6
Job opportunities / Sample Preparation & NMR Metabolomics Specialist Technician

Sample Preparation & NMR Metabolomics Specialist Technician

Salary from £26,495 to £28,936, with potential progression once in post to £32,548 a year.

The post is available in the first instance for 18 months, with a potential for extension.

As part of a £8m award from the MRC, industry and University of Birmingham, we have established a state-of-the-art metabolic phenotyping (metabolomics) facility to conduct research in human health and disease. Phenome Centre Birmingham (PCB) applies two Bruker 600 MHz NMR spectrometers, eleven liquid chromatography-mass spectrometers (LC-MS), liquid handling robots and high specification computational infrastructure to better understand metabolic perturbations in disease, toxicology and exercise science. The facility has the capacity and capability to conduct tens of thousands of metabolite analyses per year, creating genuinely ‘Big Data’ and societal impact.

We seek to recruit a full-time highly motivated Sample Preparation & NMR Metabolomics Technician to join the team of nine scientists at the PCB. The successful candidate will contribute to fulfilling the research objectives of the centre with a focus on sample management, the preparation of human biofluid and tissue samples by applying liquid handling robots, and the application of NMR spectrometry for metabolic phenotyping. They will lead the data collection of large scale NMR based metabolomics studies in collaboration with researchers within and external to the University, including academic, industry, scientific instrument manufacturer scientists.

Applicants should at least hold a Bachelor’s degree (in a physical science), with hands-on experience in sample preparation robotics and small molecule NMR spectroscopy.

Informal enquiries can be addressed to Dr Andrea Mitchell on tel: +44 (0)121 414 4062 or a.m.mitchell@bham.ac.uk or Professor Mark Viant on tel: +44 (0)121 414 2219 or email: M.Viant@bham.ac.uk
 
For further details on the Phenome Centre Birmingham, visit: https://www.birmingham.ac.uk/research/activity/phenome-centre/index.aspx

Applicants are invited to apply on-line via our e-recruitment system here. Please quote post number 51680 in any correspondence.

Closing date: 24 June 2018

Job Reference: 51680

Valuing excellence; sustaining investment
7
Job opportunities / Research Fellow in Bioinformatics/Biostatistics
Role: Research Fellow in Bioinformatics/Biostatistics
Salary: Full time starting salary is normally in the range £29,799 to £38,832. With potential progression once in post to £41,212 a year.

Job Purpose

To contribute significantly to the excellence of the ‘metabolomics ecosystem’ at the University of Birmingham, primarily contributing to the NERC Biomolecular Analysis Facility – Birmingham (NBAF-B), the UK’s national research centre for Environmental Metabolomics. Additionally, to engage with scientists in Phenome Centre Birmingham as well as Viant’s, Dunn’s and Weber’s research teams. The postholder will develop and apply expert analysis of large-scale mass spectrometry and/or NMR spectroscopy based metabolomics datasets, including experimental design, data processing, statistical analysis and/or network analysis; to contribute to the Birmingham Metabolomics Training Centre; and to undertake independent research in bioinformatics/biostatistics.

Person Specification
•   PhD or equivalent experience in Bioinformatics, Biostatistics, Chemometrics or Metabolomics (all with metabolomics or related specialism).
•   Experience in the application of statistical / computational methods to the analysis of metabolomics datasets (either mass spectrometry and/or NMR spectroscopy based).
•   Experience in a range of statistical analysis methods, including multivariate and univariate methods.
•   Experience in programming, for example scripting in R, Python, Matlab.
•   Experience in managing multiple projects simultaneously.
•   Excellent communication and interpersonal skills, including the ability to communicate complex information clearly.
•   A high level of accuracy and attention to detail.
•   Ability to work on own initiative, manage time effectively, progress tasks concurrently and work to deadlines.
•   Detailed knowledge of office safety.
•   Ability to assess resource requirements and use resources effectively.

For further information and to apply for this role, please visit: https://atsv7.wcn.co.uk/search_engine/jobs.cgi?SID=amNvZGU9MTcwMTkxNyZ2dF90ZW1wbGF0ZT03Njcmb3duZXI9NTAzMjUyMSZvd25lcnR5cGU9ZmFpciZicmFuZF9pZD0wJnZhY2Zpcm0udmFjdGl0bGU9NDczMjImcG9zdGluZ19jb2RlPTExNw==
8
Job opportunities / Research Fellow in Molecular Toxicology
Role: Research Fellow in Molecular Toxicology
Salary: Full time starting salary is normally in the range £29,799 to £38,832. With potential progression once in post to £41,212 a year.

Role Description
To contribute to the achievement of the School of Biosciences’ research vision in translational molecular toxicology by undertaking specified research activities within a thriving and well-established collaboration with a team of scientists at Unilever.

This post forms the central component of a research project with Unilever “Towards an integrated approach in defining the MoA / KE of chemicals”. As such the postholder will build upon some very large scale multi-omics studies (transcriptomics and metabolomics) that have recently investigated the effects of chemicals on the health of Daphnia magna, specifically with the goal to discover modes of action and putative key events. The postholder will focus on the translation of these putative key events into a robust mechanistic understanding of toxicity; and additionally to collaborate with scientists from Unilever to integrate this new knowledge into their chemical safety science. Significant opportunities exist to more deeply mine the wealth of omics data that has been generated within the earlier laboratory investigations. The role will be to conduct Daphnia toxicity exposure studies focusing on high resolution concentration-response studies, conducting targeted gene expression and metabolite assays, undertake extensive statistical analyses to build and characterise the key event relationships within an Adverse Outcome Pathway framework, and ultimately generate new knowledge in toxicology.

Person Specification
•   PhD or equivalent experience in Molecular (Eco)Toxicology or a related discipline.
•   Experience in chemical exposure studies, ideally in vivo studies of aquatic organisms.
•   Experience in the measurement of gene expression and/or targeted metabolite analysis using LC-MS/MS approaches.
•   Experience in a range of univariate and multivariate statistical analysis methods.
•   Experience in managing multiple tasks simultaneously.
•   Excellent communication and interpersonal skills, including the ability to communicate complex information clearly.
•   A high level of accuracy and attention to detail.
•   Ability to work on own initiative, manage time effectively, progress tasks concurrently and work to deadlines.
•   Detailed knowledge of office safety.
•   Ability to assess resource requirements and use resources effectively.

For more information and to apply, please visit: https://atsv7.wcn.co.uk/search_engine/jobs.cgi?SID=amNvZGU9MTcwMTkyMiZ2dF90ZW1wbGF0ZT03Njcmb3duZXI9NTAzMjUyMSZvd25lcnR5cGU9ZmFpciZicmFuZF9pZD0wJnZhY2Zpcm0udmFjdGl0bGU9NTUyMjUmcG9zdGluZ19jb2RlPTExNw