Tools on The Carpentries

My Favorite tool - A Coding Sandbox

Thu, 21 Dec 2017 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

My favorite tool is repl.it, a ‘sandbox’ tool to help me test and refine Python code.

Why do I like it?

It is an online tool for testing/running code. It allows you to write and run code in a number of different languages, and see the results. No R support I’m afraid, but it does have Python (2 and 3), Ruby, Haskell, Go, JavaScript and many more.

My Favorite Tool - Asking for Help

Tue, 28 Nov 2017 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

My favorite tool is asking for help. You may not think of it as a tool, but it’s something I use frequently to solve a wide range of problems, so I think it qualifies. Whether it’s saying, “I don’t know what to do next – does anyone have any ideas?” when teaching, or cold-calling people to see if they’ll host a workshop, asking for help has probably done more for me than Emacs and version control combined.

My Favourite Tool: OpenRefine

Mon, 30 Oct 2017 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

My favorite tool is OpenRefine.

OpenRefine all the way, baby! I’m the curator of eagle-i, an RDF open access repository of stem cells, viruses, mice, core facilities, lab equipment and people. I use OpenRefine to facet by URI, by date, by label, to clean the data up, search for anomalies and export in csv, Excel or whatever format is needed for my purpose.

I use OpenRefine’s General Refine Expression Language functionality (GREL) to perform complex search and replace, to transform the data, to break up and combine strings.

My Favourite Tool: Git/GitHub

Wed, 25 Oct 2017 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

My favorite tool is …

I love Git and GitHub.

I only use them for work I care about. Examples include lesson development for R workshops, my recent performance review packet, and collaborative projects on species distribution modeling. Oh, and Software Carpentry workshop websites (obviously).

Why I like Git:

The version control system and the companion remote host system (GitHub or Bitbucket or CloudForge, etc.) provide a great versioning and collaboration platform, the highlights of which have been enumerated many times over and in such depth that I won’t talk about them here.

Blogging for the Carpentries - We Want to Hear From You

Mon, 16 Oct 2017 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

This is an open invitation to our community members to share their knowledge.

We have a global community working in many different disciplines using a vast range of tools. On our blog, we would like to tap into that community experience and then share that hard-won knowledge.

This kind of information could help people new to a discipline, or might inspire others to try out a tool they have never used before.

My Favourite Tool: R

Mon, 16 Oct 2017 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

My favorite tool for data analysis is R.

I have used it for a few years now, I feel at ease when I need to work with tabular data. Using R makes my work enjoyable. I can clean my data in one place - RStudio - and then work with it creating new graphics. I also enjoy learning new things in R. Its constant development gives you the chance to learn a bit more every day. This is thanks to a huge collaborative community that supports you, with quick answers, with examples, and with new packages.

How to print our lessons?

Mon, 08 May 2017 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

From the time that I joined Software Carpentry, I remember two feature requests that often showed up on our list of issues. The first one was links to help navigate the lessons and the second one was a way to print the lessons. Adding these two features was challenging because the limited information that is available as metadata by Jekyll (or Pandoc, which we used for a while). In addition, we want to have a “real” solution, instead of a workaround that is going to stop work in a few months. Although as software developers we knew that at every release of Jekyll, or any other library, that we are using exist a chance that our pipeline will break.

Plans for Windows Installer

Thu, 04 May 2017 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

In March, we had two email threads on our discuss mailing list related to nano on Windows machines The first thread was about “nano not found”, a bug on our installer that we never managed to trace. The second thread was about some “misbehaviour” of nano on Windows, and the suggestion to use Atom as the default text editor. The suggestion to use Atom started a long discussion where instructors described their reasons to use nano and why Atom is inadequate which lead us to start investigating ways to install nano properly on Windows. On May 3rd, Kate Hertweck, Maneesha Sane, Naupaka Zimmerman, Rémi Emonet and I met online to draft a plan—taking into consideration all of the feedback that was provided in the past month—to solve the problem with nano on Windows.

Software tools for unix shell: Survey and April community call

Fri, 14 Apr 2017 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

The Software Carpentry Code of Conduct includes a somewhat tongue-in-cheek reference to nondiscrimination based on “choice of text editor.” While a choice of software may seem trivial, this particular discussion has led to more than one heated exchange among programmers. In fact, the Discuss list in March was very active concerning issues with the Windows installer, which provides access to the nano text editor through Git for Windows (used in both the Software Carpentry Shell and Git lessons). That discussion eventually transitioned to consideration of alternative software tools we might consider using and moved over to GitHub, where you can read more about the opinions and options voiced by participants.

Cookie Cutter

Tue, 10 Feb 2015 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

I was first introduced to William Stafford Noble's paper "A Quick Guide to Organizing Computational Biology Projects" when Ivan Gonzalez and I taught Harvard last November. Noble describes how scientists in Computational Biology should set up their project folders so code, results, outputs, figures, and papers are all in easily understandable locations. He also writes about how one should run experiments (using driver scripts) to make workflows reproducible, readable, and understandable to others (and your future self).

Plot This

Mon, 09 Feb 2015 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

The most useful little guide to visualization I've ever found is the decision tree created by Andrew Abela, which you can find here. Do you want to show a comparison, a distribution, a relationship, or a composition? If it's a comparison, is it among items or over time? Each choice leads to a different kind of plot, and while you may not agree with all the choices, it makes the reasoning behind them concrete.

Oh My God It's Django!

Thu, 17 Aug 2006 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

Guido just pronounced: Django is the web framework

Won't be part of the core, but will be as "standard" as PIL or NumPy
This was not what I expected the outcome of my talk would be, but hey, I'll take it ;-)
He hopes that Django and TurboGears will converge

Eric Jones: Enthought Tool Suite

Enthought does open source software and consulting for scientific computing with Python
- One of the sponsors of this conference
- Providing hosting for Software Carpentry
- Walked through traits and other offerings
Chris Mueller: Synthetic Programming with Python