User: Martin Fitzpatrick

Reputation:
180
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Location:
Birmingham, United Kingdom
Website:
http://martinfitzpatri...
Scholar ID:
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Last seen:
4 years, 5 months ago
Joined:
6 years, 6 months ago
Email:
m*****************@gmail.com

Post-doctoral bioinformatics researcher at Universiteit Utrecht, Netherlands. Previously completed a PhD at the University of Birmingham, UK in the metabolomics of inflammatory diseases. Keen open-source programmer and developer behind Pathomx a workflow-based desktop analysis tool, developed to automate the processing of NMR spectra. Working mainly in Python, MATLAB and R.

Posts by Martin Fitzpatrick

<prev • 9 results • page 1 of 1 • next >
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Answer: A: Alternatives To Galaxy For Wrapping Command Line Tools In A Graphical User Inter
... Bit late to this party but I've recently developed Wooey a simple tool for creating "Web UIs" for command line scripts. It's based on the similarly named Gooey which automatically creates standard desktop UIs from Python commandline scripts. For Python scripts Wooey inherits that ability and allows ...
written 4.5 years ago by Martin Fitzpatrick180
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Comment: C: Pathomx: Metabolic Pathway Visualisation And Analysis
... I only just noticed your comment here Istvan. I've signed up for Metastars and will take a look! Thanks ...
written 4.9 years ago by Martin Fitzpatrick180
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Comment: C: Pathomx: Metabolic Pathway Visualisation And Analysis
... Thanks Lluis. I've updated and extended it a bit - is there something in particular you're looking to know? There is a new website up at http://pathomx.org with a bit more information and I've started bulking out the API documentation for plugin-building. Any suggestions are most welcome. ...
written 5.6 years ago by Martin Fitzpatrick180
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Comment: C: Pathomx: Metabolic Pathway Visualisation And Analysis
... Yep David. I've written it from the ground up to be as 'generic' as possible. Each of the 'tools' you see in the workflow define the inputs they'll take, process them and output them. So far all the tools use a generic 'DataSet' object but implementing a data holder for BLAST data should be fairly t ...
written 5.6 years ago by Martin Fitzpatrick180
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Comment: C: Pathomx: Metabolic Pathway Visualisation And Analysis
... We have a new version of MetaPath ready for release and a publication following along shortly. Should I update (edit) this post or post a new entry? Thanks ...
written 5.8 years ago by Martin Fitzpatrick180
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Comment: C: Pathomx: Metabolic Pathway Visualisation And Analysis
... Thanks for giving it a go Manu. What errors did you get? Did you install Graphviz (http://www.graphviz.org/) beforehand? I'm working on removing that as a dependency but it's currently needed for the layout. ...
written 6.4 years ago by Martin Fitzpatrick180
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Comment: C: Improving Site Navigation: Adding Definitions To Tags
... It could be set up on a subset of tags to begin with (not every tag would need this information just the major ones)? ...
written 6.4 years ago by Martin Fitzpatrick180
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Comment: C: Improving Site Navigation: Adding Definitions To Tags
... It might work to use snippets from Wikipedia in the first instance (the license allows use of the text as long as appropriately credited) which can be edited if needed later. Using medhat.helmy77's example of chip-seq doing a Wiki search against that returns this page: http://en.wikipedia.org/wiki/C ...
written 6.4 years ago by Martin Fitzpatrick180
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Tool: Pathomx: Metabolic Pathway Visualisation And Analysis
... What is Pathomx? Pathomx is a workflow-based metabolomics analysis tool. It has been developed as part of my PhD to enable rapid visualisation and interpretation of metabolic data within a pathway context. The latest release (v2.5) provides a number of novel features: Workflow based data explor ...
pathway python visualization tool written 6.4 years ago by Martin Fitzpatrick180

Latest awards to Martin Fitzpatrick

Popular Question 5.4 years ago, created a question with more than 1,000 views. For Pathomx: Metabolic Pathway Visualisation And Analysis
Autobiographer 5.5 years ago, has more than 80 characters in the information field of the user's profile.
Appreciated 6.4 years ago, created a post with more than 5 votes. For Pathomx: Metabolic Pathway Visualisation And Analysis

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