standage.github.io
Daniel S. Standage: Curriculum vitaeAcademic home page and CV for Daniel S. Standage
http://standage.github.io/
Academic home page and CV for Daniel S. Standage
http://standage.github.io/
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Daniel S. Standage: Curriculum vitae | standage.github.io Reviews
https://standage.github.io
Academic home page and CV for Daniel S. Standage
standage.github.io
Daniel Standage
http://standage.github.io/index.html
Daniel S. Standage. University of California, Davis. Davis, CA 95616. Lab for Data Intensive Biology. Hi, I'm Daniel, a research scientist with interests in bioinformatics, genome biology, and research software engineering. I am committed to open, transparent, and reproducible research, and to established software engineering practices to the extent that they facilitate these ends. I also enjoy mentoring and teaching, both in the classroom and in less structured settings. See my curriculum vitae. My appr...
AEGeAn Toolkit
http://standage.github.io/AEGeAn
AEGeAn source code on GitHub. Integrated genome analysis toolkit. The AEGeAn Toolkit is designed for the A. Notations. The toolkit includes a variety of analysis programs as well as a C library whose API provides access to AEGeAn's core functions and data structures. AEGeAn is free to use and is released under an unrestrictive open source license. Daniel S. Standage and Volker P. Brendel (2012) ParsEval: parallel comparison and analysis of gene structure annotations. 187, doi:10.1186/1471-2105-13-187.
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AEGeAn Toolkit
https://brendelgroup.github.io/AEGeAn
AEGeAn source code on GitHub. Integrated genome analysis toolkit. The AEGeAn Toolkit is designed for the A. Notations. The toolkit includes a variety of analysis programs as well as a C library whose API provides access to AEGeAn's core functions and data structures. AEGeAn is free to use and is released under an unrestrictive open source license. Daniel S. Standage and Volker P. Brendel (2012) ParsEval: parallel comparison and analysis of gene structure annotations. 187, doi:10.1186/1471-2105-13-187.
Pandas: querying a data frame and the `SettingWithCopyWarning` message | BioWize
https://biowize.wordpress.com/2015/06/18/pandas-querying-a-data-frame-and-the-settingwithcopywarning-message
Tidbits of software wisdom for the modern biologist. June 18, 2015. Pandas: querying a data frame and the `SettingWithCopyWarning` message. That said, I still have a lot to learn regarding Pandas. Earlier today I was doing some simple operations—taking a subset of a data frame and creating a new column by applying a transformation to another column—and I kept getting a cryptic. Message. Here’s a dummy example that reproduces the message. Variable and want those changes reflected in the original. Subset t...
Reproducible software behavior with random seeds | BioWize
https://biowize.wordpress.com/2015/08/05/reproducible-software-behavior-with-random-seeds
Tidbits of software wisdom for the modern biologist. August 5, 2015. Reproducible software behavior with random seeds. Time the software runs. How can one verify the behavior of such a program in an automated fashion? Alternatively, what if you find a case in which the program produces incorrect output? How do you reproduce that specific case for troubleshooting and testing? The behavior of a programming language’s random number generator and related features can be predictable with the use of a. Here is...
Daniel Standage | BioWize
https://biowize.wordpress.com/author/byuhobbes
Tidbits of software wisdom for the modern biologist. My blogging days at BioWize are done. My latest posts are at http:/ standage.github.io. Assert statements: software crumple zones. October 2, 2015. Reproducible software behavior with random seeds. August 5, 2015. My comments on “software solutions for big biology” paper. July 24, 2015. Basic summary stats for all genomes at NCBI. July 24, 2015. Pandas: querying a data frame and the `SettingWithCopyWarning` message. June 18, 2015. May 28, 2015.
Task automation with bash and parallel | BioWize
https://biowize.wordpress.com/2015/03/23/task-automation-with-bash-and-parallel
Tidbits of software wisdom for the modern biologist. March 23, 2015. Task automation with bash and parallel. The easiest way to automate repetitive command-line tasks is with the bash for loop. Assuming you’ve exercised at least a minimal amount of discipline in naming your data files, it should be straightforward to apply the same command to many different data files. The basic structure of a for loop is as follows. For i in 1 2 3 4 5; do someCommand data$i.fastq output$i.txt; done. For i in 1 2 3 4 5.
Literate programming, RStudio, and IPython Notebook | BioWize
https://biowize.wordpress.com/2015/03/13/literate-programming-rstudio-and-ipython-notebook
Tidbits of software wisdom for the modern biologist. March 13, 2015. Literate programming, RStudio, and IPython Notebook. Which provides excellent 2-day workshops introducing these topics at a beginner level to scientists. My point is that if you’re writing software to be distributed amongst collaborators and colleagues, there are well established software engineering practices to make this a painless experience for everyone involved, and learning the basics doesn’t require much work. But it wasn’t...
Embeddable image links for asciicasts | BioWize
https://biowize.wordpress.com/2015/05/14/embeddable-image-links-for-asciicasts
Tidbits of software wisdom for the modern biologist. May 14, 2015. Embeddable image links for asciicasts. A couple years ago I stumbled across ascii.io. Which is no asciinema.org. A phenomenal tool for recording terminal sessions. Command-line mechanics is one of the biggest barriers of entry for scientists learning informatics, and I’ve found this tool to be much more useful than screenshots or copy/paste text for communicating terminal behavior to students and colleagues. The ability to embed asciicasts.
GitHub now renders IPython/Jupyter Notebooks! | BioWize
https://biowize.wordpress.com/2015/05/21/github-now-renders-ipythonjupyter-notebooks
Tidbits of software wisdom for the modern biologist. May 21, 2015. GitHub now renders IPython/Jupyter Notebooks! I’ve written before about literate programming. And how I think this could be a big game changer for transparency and reproducibility in science, especially when it comes to data analysis (vs more traditional software engineering). Well, GitHub announced recently. Leave a Reply Cancel reply. Enter your comment here. Fill in your details below or click an icon to log in:.
Leading zeros with bash brace expansion | BioWize
https://biowize.wordpress.com/2015/05/28/leading-zeros-with-bash-brace-expansion
Tidbits of software wisdom for the modern biologist. May 28, 2015. Leading zeros with bash brace expansion. I use bash brace expansion extensively, both in interactive terminal sessions and in shell scripts. The idea is pretty simple: the simple syntax. Is a shortcut to an array containing all of the integers from. Inclusive. I’ve used this syntax several times in examples on this blog, including a recent post about task automation in bash. 10; echo {8.10} 8 9 10 echo {08.10} 08 09 10. You are commentin...
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United We Stand, Divided We Fall. Welcome to Stand Against Walker. We are an organization dedicated to fighting Wisconsin Governor Scott Walker and his GOP counterparts in the House and Senate. We hope that this site will be a portal for any information you will need and help keep you informed on the issues. Please check back regularly as the site is updated often. Feel free to register. It's free and gives you access to the blogs and image galleries. Thursday, August 13, 2015 5:48:39 AM. Hillary Clinton...
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Daniel S. Standage: Curriculum vitae
205A Simon Hall, Indiana University. 212 South Hawthorne Drive. Bloomington, IN 47405. Iowa State BCB Program. I am a Ph.D. candidate in the research groups of Volker Brendel (Indiana University). And Amy Toth (Iowa State University). 2010 — 2015. PhD in Bioinformatics and Computational Biology. In residence at Indiana University since July 2012. 2003 — 2010. With minors in Mathematics. Duvick JP, Standage DS. Brendel VP (2012) ParsEval: parallel comparison and analysis of gene structure annotations.
The Standage Family
Thursday, January 21, 2010. We took Tyler and Ashton up to Sunrise Skii Restort yesterday. We couldn't have asked for a better day. Whene we arrived at the hotel their was NO snow what-so-ever but when we woke up we had a Winterwonderland! The boys did real well. It was so much fun! We can't wait to do it again! Saturday, December 5, 2009. Our Kids with Santa 12/4/2009. Subscribe to: Posts (Atom). A Family Who Loves To Have Fun! View my complete profile. Andy and Melanie Guymon. Evan and Driel's Family.
dominic.standage.net - Dominic Standage - Biography
Welcome to dominic.standage.net. Here, you'll find my CV. A list of publications. And a brief biography below. I'm a research scientist at the Centre for Neuroscience Studies. Canada, where I work with Gunnar Blohm. In the Computational Neuroscience Lab and Martin Pare in the Visual Information Processing Lab. Both labs are in the Department of Biomedical and Molecular Sciences. I completed my PhD at the Faculty of Computer Science. East Regional Soccer League.
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JEFF'S ART PAGE
This blog page is a sample of my work as an artists. Hope all my visitors enjoy! Saturday, December 17, 2011. Sunday, April 11, 2010. Tuesday, January 5, 2010. Monday, April 6, 2009. Wednesday, August 6, 2008. Tuesday, April 8, 2008. Won Maricopa Community College Chancellor Art Show "Artist of Promise". Tuesday, November 20, 2007. Wednesday, November 7, 2007. Tuesday, August 14, 2007. Monday, August 13, 2007. Subscribe to: Posts (Atom). Contact me at jdstandage@yahoo.com. View my complete profile.
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