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Michael Crusoe
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Calling Taverna Workflows from iPython Notebook

The myGrid team are pleased to announce the release of an alpha version of a Python package that allows the running of Taverna Workflows within an iPython Notebook.

The tavernaPlayerClient package, currently at version 0.06 can be installed from PyPi. For example, using

pip install tavernaPlayerClient

The Client allows you to connect to a Taverna Player and to select and run workflows. You can use data from the iPython Notebook as inputs to the workflow run, and use the results of the run in later cells in your notebook.

A demonstration video as at

An example notebook is available at

A more complex example showing the chaining of workflows is at

This work was done with the help of Youri Lammers  from Naturalis in the Netherlands  and Ross Mounce  from the University of Bath, UK and was partially carried out at the pro-iBiosphere Data Enrichment Hackathon - 

For more information, comments or questions, please contact

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Love this tool, makes any Python project better.

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For those who can support Free Software with money, here is a worthy cause!
This is an extremely worthwhile cause. If you use Android or any number of free software projects, please, donate!

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Position available for Bioinformatics Software Developer
Our laboratory at Cincinnati Children’s Hospital is developing software for analysis of Next-Generation Sequencing data for use in bioinformatics/ epigenomics/ transcriptomics research. 
We are looking for a software developer who has experience or interest in full stack web software development with a focus on designing, developing and maintaining production software systems in data-intensive settings, aimed primarily at scientific applications. The developer must be able to adapt to changing specifications and priorities, be willing to take initiative and ownership of their work, and learn.
The ideal candidate should have experience in majority of the following areas: 
• Working on server-side components (including clusters and/or clouds) or client-side (web UI) components,
• Modern software engineering practices such as automated testing and continuous integration/deployment. 
• Server side JavaScript (e.g. Node.JS) and modern JavaScript UI frameworks such as AngularJS or ExtJS
• SQL or NoSQL databases (e.g. MongoDB)
• REST API design and implementation 
• Bioinformatics
The successful candidate will be working on enhancement of existing software (see under a guidance of an experienced developer. 
Opportunities for Master’s or PhD thesis research are available.
For additional information, please contact Artem Barski 
More about Cincinnati Children’s:
Visa support may be available for foreign candidates.

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Great talk from a former colleague
This is a talk I gave recently about how to survive in technical jobs. It's mostly aimed at women but a bunch of men have told me it was useful for them too.

The speaker notes have most of the content.

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New chat for (#scientific, #bioinformatics) #workflow tool makers and implementers, to share experiences, discuss best practices and solutions of technical nature. Kindly hosted at the common workflow language github organization. #CommonWL #workflows

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Our new community paper about the awesome BioJS community and there involvement in Galaxy.

Installing BioJS components in Galaxy is as simple as it can get!

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More travel adventures!

Testing the new G+ collections feature
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