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BioWize | Tidbits of software wisdom for the modern biologistTidbits of software wisdom for the modern biologist (by Daniel Standage)
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Tidbits of software wisdom for the modern biologist (by Daniel Standage)
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BioWize | Tidbits of software wisdom for the modern biologist | biowize.wordpress.com Reviews
https://biowize.wordpress.com
Tidbits of software wisdom for the modern biologist (by Daniel Standage)
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:.
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...
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.
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...
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The Book of Standage: February 2015
http://bookofstandage.blogspot.com/2015/06/february-2015.html
Sunday, June 14, 2015. We blessed Joseph on February 1st. He was blessed to be healthy and strong, to be strong in the service of the Lord, with discernment and loyalty to God, the ability to sacrifice, enthusiasm for life and optimism, as well as determination to testify and study the scriptures. We made homemade donuts one snowy sunday. Heather loves her baby brother. Daddy's first attempt at a braid. I think he did pretty good! Traditional heart-shaped pancakes and pizza for Valentines day! We had alm...
The Book of Standage: November 2013
http://bookofstandage.blogspot.com/2013_11_01_archive.html
Wednesday, November 27, 2013. Ever since that Thanksgiving, stinky cheese nights have become a Thanksgiving break standard for Stephanie and I. We like to try new things, but we always try to include a good raunchy blue cheese. Monday, November 18, 2013. Always able and willing to smile and be happy- even when she's so sick! Sunday, November 17, 2013. Oh Josh, you are adorable! Do you know that? Yes, of course you do, I tell you several times a day! You are snuggly and sweet, and you know it too! You are...
The Book of Standage: January 2015
http://bookofstandage.blogspot.com/2015/01/january-2015.html
Friday, January 30, 2015. How is it that another year has already gone by? It seems like the years have been flying by lately! We actually spent most of the month sick. The beginning of the month all the kids got Bronchiolitis and double ear infections. Both Josh and Joey had to be on the nebulizer several times a day. Thankfully, because I had all the equipment at home, we were able to avoid the hospital with Joseph. During this rough time, Daniel was gone at a conference. Yay me! Daniel got to particip...
The Book of Standage: August 2014
http://bookofstandage.blogspot.com/2014_08_01_archive.html
Sunday, August 31, 2014. It is so unreal that my little baby is going to Kindergarten and loving it! She is making new friends, and enjoys her time there. She is a little ornery some days, I just try to be patient knowing that she is probably tired from the extra long day. The school goes from 8:30a-3:50p. WAY too long for a five year old! Especially hogging all the balls. And the cool oil thing. Mom made a very intricate marble tower with ALL the pieces! Heather is hiding. Can you find her? Josh had a h...
The Book of Standage: December 2013
http://bookofstandage.blogspot.com/2013_12_01_archive.html
Friday, December 27, 2013. Getting ready to act out the nativity. Josh is pretty excited to play the part of Joseph. And Mary was great with child. What a cute donkey! Luvin' on the baby. He's going to make a great daddy someday. I was the angel. Josh couldn't get enough of the donkey rides. All the gifts and lights. I loved my little set up this year. This is what the kids saw when they first came down. We tried to help them remember that this was all about Jesus. Going through the stockings. We started...
The Book of Standage: March 2015
http://bookofstandage.blogspot.com/2015/06/march-2015.html
Sunday, June 21, 2015. Winter took its time this year, but when it came it came strong! Church was cancelled on March 1st, so we spent the morning having our own little church service (the kids sharing their testimonies on the "stand" with the "microphone") and then built some snowmen with the wonderfully packable snow (most of the snow this year was dry powder). Kids got a new bunkbed with personalized bedding. Best way to celebrate birthday is to share cupcakes with friends! And a few random pics.
The Book of Standage: February 2014
http://bookofstandage.blogspot.com/2014_02_01_archive.html
Thursday, February 27, 2014. We had a bit of warmer weather recently. Yeah, it got up to about 40°F. Before it snowed again. Grrrbut that's another story. It is winter after all. The kids took advantage of it by splashing in the slush puddle (a hole in the ice), and playing in the mud.Again. Only this time.they really. Played in the mud. And I let them. Why did I let them? I just love cleaning up mud.not! Oh well. They had a lot of fun at least. In other news, Josh is a BIG BOY NOW! On the day before Val...
The Book of Standage: January 2014
http://bookofstandage.blogspot.com/2014_01_01_archive.html
Monday, January 27, 2014. Powder party in the kids' room. The kids were making a huge ruckus banging on pots and pans in their room this morning. While Stephanie was getting dressed and making the bed, the noise finally let up, giving her a few moments of peace and quiet. However, it was a bit too. Quiet, and when she finished getting dressed Stephanie decided to investigate. This is what she found. Seriously, Gold Bond powder? Don't even try to play the innocent card! Saturday, January 25, 2014. When th...
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Bio Wizardry: cauterizing the bleeding edge
Bio Wizardry: cauterizing the bleeding edge. Bioscience is happening now that was science fiction 10 short years ago. Is it sensible? How does the weirdness of our systems change the game? I don't care about what we believe. Because that interferes with thinking. I care about what works. Dept of the Blitheringly Obv. Wednesday, September 18, 2013. All the posts are there, and all your wise and lovely comments. And I hope it doesn't get hijacked, like this site did. Tuesday, February 19, 2013. What's usef...
Biowizardry: Cauterizing the Bleeding Edge | of medicine, science and adaptation - especially neurology, immunology and related disabling conditions
Biowizardry: Cauterizing the Bleeding Edge. Of medicine, science and adaptation - especially neurology, immunology and related disabling conditions. Biowizardry: Cauterizing the Bleeding Edge. Raquo; Home Page. A national Pain Crisis Protocol is imperative. January 14, 2016. Dept of the Blitheringly Obv. The main function of the ER is to Continue reading. →. Mitochondria get nasty when they get hurt. June 10, 2015. This is the full text of a very dense little article with a lot of gold embedded in it:.
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BioWize | Tidbits of software wisdom for the modern biologist
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...
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