Mary Mangan holds a Ph.D. from the University of Rochester, and has performed her post-doctoral research with The Jackson Laboratory Mouse Genome Informatics group. Later she became an Application Scientist and Scientific and Technical Liaison for Incyte Genomics and Proteome, Inc. and AstraZeneca.
Throughout her career Dr. Mangan has been involved with bioinformatics from the the end-user, biologist facing perspective. She successfully founded and operated a company called Biological Software Testing Services, Inc. and later became a founding member of the OpenHelix company. This company has been recently acquired by the the Cambridge Healthtech Institute and has become a division of Bio-IT World.
She is among the few bioinformaticians that have an up-close and unique insight into what takes place in the long-tail of bioinformatics sciences where large groups of life scientists with little computational background try to apply highly sophisticated methodologies in their work.
Dr. Mangan is a very early adopter of Biostars and is active user and moderator on our site. She writes under the pseudonym of Mary
Mary Mangan of OpenHelix
Funny, I thought that my job was so different that it might not be useful to most people. I'm not writing code. But perhaps some folks would be interested in some of what I'm doing. I'm definitely on the end-user side of bioinformatics, and heavily into training and outreach. I also do a lot of software testing. So I'll describe my tools from that perspective.
What hardware do you use?
Windows PC, running Win7. I also have a Surface to test Win8 and an Android phone for mobile items.
What is your text editor?
I started using Notepad++ based on a tip from the Software Carpentry workshop I attended.
What software do you use for your work?
Mostly browsers and Wordpress. And Tweetdeck--heh.
But some people are also interested in how we make the little videos we do. I have a tool called "Jing" for short stuff and quick screen caps that's great: http://www.techsmith.com/jing.html I sent in a bug report to a website recently with a short video to illustrate it (with the steps in text form as well), and the developer replied: "It's rare to get such a detailed and clear bug report :)"
We are big fan of all of the TechSmith tools, actually, they are very good and reasonably priced for what we do. For longer videos and other graphics stuff, we use their SnagIt and Camtasia, depending on the needs.
What do you use to create plots and charts?
I am always looking for web-based tools for this. The kind of things I need are more along the lines of the lightweight tools I mentioned in a recent post:http://blog.openhelix.eu/?p=19855 . Mutation Mapper, DomainDraw, MyDomains. I just started to play with the TreeMap at REVIGO, and I'm liking that.
What do you consider the best language to do bioinformatics with?
What bioinformatics tools/software do not get enough recognition?
I think visualization tools get short shrift. I don't work in code and with command lines much, and as someone who came into this from the biology side, I need better visualizations. My current sleeper favorites are the Caleydo tools: http://caleydo.org/
See all post in this series https://www.biostars.org/t/uses-this/
To be notified of new post in the series follow the first post: Jim Robinson of the Integrative Genomics Viewer (IGV) uses this