As described in a previous message I am currently recruiting a Data Scientist to fill the position of a senior postdoctoral research fellow. Any applicant should have extensive experience (PhD+) in one or more of the following: Biostatistics, Bioinformatics, Cheminformatics, Data Management, or Machine Learning - and must be a proficient programmer in a standard scripting language (preferably Python). Being able to write Matlab, R, SAS scripts would be a bonus. http://tinyurl.com/gw63a4w
I have had a few inquiries about the above position and it seems that potential applicants are uncomfortable with the idea of not being given a specific project to work on. There are so many areas of metabolomics data analysis that either require radical new approaches, significant further research, or a simply not provided. So should anyone need a nudge in the right direction, here are a few projects that I will be engaging with in the near future and with which I would like some help.
1) Next generation of software for the removal of within/between batch systematic variation. Building on the success of my QC-RSC algorithm ( http://link.springer.com/article/10.1007/s00216-013-6856-7 ). Moving to a hierarchical multivariate generalized model. 2) Radically reinventing the data analysis "workflow" moving from a depressingly constraining linear "data dredging" (algorithm dredging) approach of current online solutions (galaxy, knime, metaboanalyst) to a directed nonlinear workflow based on study design and with the aim to identify the correct statistical model to analyse your data with based clear assumptions on data type and distribution (similar to scikit learn https://goo.gl/images/B2yrCk and Laerd Statistics https://statistics.laerd.com/features-selecting-tests.php ) 3) A non-linear approach to the multi-block problem integrating multi-system data using Neural Networks. 4) Feature Selection and Model optimization using Evolutionary Computation (GAs / GPs ) 5) Non-linear cluster-based time-series analysis. Investigating metabolite sub-trajectories as an alternative to cross-sectional biomarkers. leading of N-of-1 personalized medicine. 6) Web-based interactive data visualization of complex system interactions using a combination of network analysis, pathway mapping and classical visualization techniques. 7) Developing web-based training resources on Experimental Design and Data Analysis using Python and Jupyter.
There are many more floating around, but hopefully this will give people an idea of the opportunities in my lab over the next 5 years or so.
I have recently been awarded ~$3M to set up a metabolomics facility: The Centre for Integrative Metabolomics & Computational Biology at Edith Cowan University in Perth Australia (www.cimcb.info). This is a Thermo Fisher sponsored proof-of-concept lab housing state-of-the-art mass spectrometry equipment backed up by a comprehensive suite of high-performance OSX workstations and access to multiple supercomputers.
My lab is fitted out with the highest quality Thermo-Fisher instrumentation including an LC-Q Exactive MS, GC-Q Exactive MS, and a Quantiva QQQ LC-MS, which is supported by a comprehensive computational biology capability for the provision of reproducible data, mathematical modelling, and biological interpretation. Our focus on robust workflows, quality control, and intuitive data integration, will allow vibrant and innovative research to flourish, encouraging stimulating interactions between biological, medical, and computational scientists.
I am seeking to employ a research fellow with a PhD in Mass-Spectrometry based Metabolomics, Analytical Chemistry, Biochemistry, or related discipline, with an exceptional track record in metabolomics research and demonstrable expertise in Gas Chromatography - Mass Spectrometry (GC-MS). The primary role of successful applicant will lead the use and development of the centre’s Thermo Q Exactive Orbitrap GC-MS as a tool for metabolomics analysis – probably the best high-resolution mass spectrometer in production. There will be significant opportunity, and expectation, for the successful applicant to develop their own research program, lead research projects, and grant applications.
It is expected that the successful applicant will bring along experience in a particular area of applied research to complement their understanding of GC-MS metabolomics. That area is to be proposed (and pitched to me) as part of the job application. Our centre will focus on 3 primary areas of applied research: (i) Sports/Exercise/Human Exposome; (ii) Human integrated ‘omics with particular focus on microbiome/host metabolite interaction (iii) Marine / Ecological metabolomics / systems biology. These areas reflect the expertise of the current team and local collaborators. However, given a sufficiently strong case I am willing to let the research fellow pursue any avenue of metabolomics research.
The successful applicant must, to a large degree, be self-reliant. There will be a range of analytical chemistry MS expertise at the Centre but is expected that this person would lead the GC-MS method development in all areas (as a management position). Of course the trade-off is that you will have some of the best computational support in the metabolomics community (Design of Experiments, quality control, signal processing, statistics and bioinformatics) and the opportunity to learn to become an expert in these skills. I will be teaching all my staff to program in either Matlab or Python.
I was a post-doctoral researcher for over 12 years before I "got my break", so I am well aware of how hard it is to get a successful career off the ground. My role as supervisor for this position is to accelerate this career process by providing guidance, support, and allowing as much time as possible for the successful candidate to translate their research ideas into a career trajectory. Inevitably, there will be a certain amount of quid-pro-quo work on projects from other team members and possibly contract work. However, I can pretty much guarantee that 50% of your time will be spent on research projects led by the successful candidate, but with the full support and resources of the centre. I have also worked very hard to get the salary to a level that I consider reasonable.
1) It is a 3-year fixed term appointment, which can/will be extended if the applicant is considered successful. 2) The salary is AU$95,979 – AU$113,978 (~US$71,500 - ~US$85,000 ; Euro €67,000 - €79,600 ; GBP £56,000 - £66,700 ) 3) 17% University superannuation (pension) contribution. 4) There is funding for a working visa. 5) There is funding for relocation.
After working in Metabolomics for over 18 years, in 5 countries, on over 60 projects, as a computer scientist and biostatistician, I have finally made it to full professor. I have also recently been funded ~$3M to set up a lab. So I am now the director of the Centre for Integrative Metabolomics & Computational Biology at Edith Cowan University in Perth Australia (www.cimcb.info). This is a Thermo Fisher sponsored proof-of-concept lab housing state-of-the-art mass spectrometry equipment backed up by a comprehensive suite of high-performance OSX workstations and access to multiple supercomputers.
As far as I am aware, I am in a unique situation. CiM-CB will be the only metabolomics lab in the world that is lead by a computer scientist. Unsurprisingly, I have a very data-centric research vision, with a clear focus on robust workflows, quality control, intuitive data integration, and machine learning, which will hopefully allow vibrant and innovative research to flourish, encouraging stimulating interactions between computational, biological, medical, and scientists.
So, I am currently recruiting a Data Scientist to fill the position of a senior postdoctoral research fellow. Any applicant should have extensive experience (PhD+) in one or more of the following: Biostatistics, Bioinformatics, Cheminformatic, Data Management, or Machine Learning – and must be a proficient programmer in a standard scripting language (preferably Python). Being able to write Matlab, SAS scripts would be a bonus (R “programmers” should learn Python before applying … only joking!). I did my PhD in C++ & Fortran (Object-Oriented Artificial Neural Networks and Genetic Algorithms in Chemometrics) so any hardcore programmers would also be welcome.
Other than that, all I ask is that you are highly motivated team player, with a rich imagination and some crazy off-the-wall ideas for pushing forward the field of data science in metabolomics. It doesn’t have to be math based either; I have some nascent ideas on how to move data visualisation into VR, developing teaching aids using Jupyter, and radically reinventing online data science workflows. Any and every idea will be enthusiastically considered.
I was a post-doctoral researcher for over 12 years before I “got my break”, so I am well aware of how hard it is to get a successful career off the ground. My role as supervisor for this position is to accelerate this process by providing guidance, support, and giving as much time as possible for the successful candidate to translate their research ideas into a career trajectory. Inevitably, there will be a certain amount of very tedious PLS-DA modelling; many frustrating conversations with clinicians explaining why an N of 10 is a waste of time, and arguments with reviewers about why we should no longer be using p-values. On the flip-side I can pretty much guarantee that the main focus of your time and efforts will be focused on radical computational method development or being first author on papers (the data-scientist curse of being constantly 2nd author will be doggedly avoided if you do the majority of the work on a paper). I have also worked very hard to get the salary to a level that I consider reasonable.
If you are still reading this then you are also probably be thinking to yourself “ECU? Where? Why?”. To that I can only reply that IMHO Metabolomics, as it thought of today, was pretty much invented in a small lab in Aberystwyth led by Professor Douglas Kell (CBE). That lab produced Professor Royston Goodacre (eminent metabolomics scientist & editor of the Metabolomics Journal), Professor Pedro Mendes (eminent systems biology scientist), myself (ex-board of directors Metabolomics Society) and several other successful academic researchers. I am not in anyway comparing myself to Doug, but it really is “what you do, not where you do it”. Perth, Australia is very isolated but I have funds for travel. It is also one of the most beautiful, sunniest, cities in the world – with beaches you would not believe.
1) It is a 3-year fixed term appointment, which can/will be extended if the applicant is considered successful. 2) The salary is AU$95,979 – AU$113,978 (~US$71,500 - ~US$85,000 ; Euro ~€67,000 - ~€79,600 ; GBP ~£56,000 - ~£66,700 ) 3) 17% University superannuation (pension) contribution. 4) There is funding for a working visa. 5) There is funding for relocation.
So if you are interested in having an adventure in Western Australia please drop me a line for further details (email@example.com) or apply online (you have to apply through the portal) http://tinyurl.com/gw63a4w I have attached a pdf of the official advert for you to print off and digest over the upcoming holidays. Closing date 22nd January.