Women in Science and Engineering

Lawrence Berkeley National Laboratory, Berkeley, California
Apr 14-15, 2014
9:00 am - 4:30 pm

General Information

Software Carpentry's mission is to help scientists and engineers become more productive by teaching them basic lab skills for computing like program design, version control, data management, and task automation. This two-day hands-on bootcamp will cover basic concepts and tools; participants will be encouraged to help one another and to apply what they have learned to their own research problems.

Instructors

Azalee Bostroem is a Senior Research and Instrument Analyst at the Space Telescope Science Institute. She is primarily responsible for organizing the development of the calibration pipelines of the two spectrographs on the Hubble Space Telescope (the Cosmic Origins Spectrograph and Space Telescope Imaging Spectrograph). She also collaborates on a project using the Space Telescope Imaging Spectrograph to derive the properties of massive stars.

Molly Gibson is a Ph.D. candidate in Computational & Systems Biology at Washington University in Saint Louis. Her research focuses on the ecological resistance and resiliency of microbial community structures and functions to perturbation by antibiotic treatment.

Katy Huff is the lead instructor for this bootcamp. She is a postdoctoral scholar in nuclear engineering at the University of California – Berkeley. She received her Ph.D. from the University of Wisconsin – Madison, where she helped found The Hacker Within.

Jessica Kerr has channeled an undergraduate physics degree into a programming career. She loves computer science, especially when it intersects with math and complexity theory. Her goals include acquiring new tastes, sharing enthusiasm, and keeping two crazy-happy children alive.

Suzanne Kiihne has diverse programming experience ranging from fMRI to bioinformatics and mobile apps. She has developed NMR methods for studying DNA and membrane protein structures, taught atmospheric science, and tested pizza recipes while living with her two kids in Switzerland, the Netherlands, and London.

Cindee Madison develops software and research methods in a neuroimaging lab at UC Berkeley. She has been working on numerous open source projects in Python for the last eight years. Her interests range from image processing and graphics to graph theory and reproducible pipelines.

Rachel Slaybaugh is an Assistant Professor of Nuclear Engineering at the University of California Berkeley where she develops radiation transport methods for application to reactors, shielding, and nuclear security applications. Rachel writes in C++, Python, and Fortran, and has research experience with massively parallel code systems.

Who: The course is aimed at female postgraduate students and other scientists who are familiar with basic programming concepts (like loops, conditionals, arrays, and functions) but need help to translate this knowledge into practical tools to help them work more productively.

Where: Lawrence Berkeley National Laboratory, Berkeley, California. To get close, you can get directions with OpenStreetMap or Google Maps. Once you're in Berkeley, take the Blue Uphill Shuttle from Berkeley to Lawrence Berkeley National Laboratory. Then, navigate to the room dedicated for your track. There are Novice, Intermediate, and Advanced tracks.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below).

Contact: Please mail admin@software-carpentry.org for more information.

Register: Seats are limited, but registration is free and open to anyone who identifies as female. To register, please go to the Eventbrite Page. Once you have registered, please fill out the skills survey so that you can be placed in a room that targets your skillset.

Tracks

Novice	Bldg. 54 Room 130	Schedule	Etherpad
Intermediate	Bldg. 15 Room 253	Schedule	Etherpad
Advanced	Bldg. 50A Room 5132	Schedule	Etherpad

Setup

To participate in a Software Carpentry bootcamp, you will need working copies of the software described below. Please make sure to install everything (or at least to download the installers) before the start of your bootcamp.

Overview

Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on Mac OS X and Linux is usually set to Vim, which is not famous for being intuitive. if you accidentally find yourself stuck in it, try typing the escape key, followed by ':q!' (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

The Bash Shell

Bash is a commonly-used shell. Using a shell gives you more power to do more tasks more quickly with your computer.

Git

Git is a state-of-the-art version control system. It lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com.

Python

Python is becoming very popular in scientific computing, and it's a great language for teaching general programming concepts due to its easy-to-read syntax. We teach with Python version 2.7, since it is still the most widely used. Installing all the scientific packages for Python individually can be a bit difficult, so we recommend an all-in-one installer.

SQL

SQL is a specialized programming language used with databases. We use a simple database manager called SQLite, either directly or through a browser plugin.

Windows

Software Carpentry Installer

For an all-in-one installer:

Download the installer.
If the file opens directly in the browser select File→Save Page As to download it to your computer.
Double click on the file to run it.

Editor

Notepad++ is a popular free code editor for Windows. Be aware that you must add its installation directory to your system path in order to launch it from the command line (or have other tools like Git launch it for you). Please ask your instructor to help you do this.

Git Bash

Install Git for Windows by download and running the installer. This will provide you with both Git and Bash in the Git Bash program.

Python

Download and install Anaconda CE.
Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

SQLite

Download the sqlite3 program and put it in the directory where you are running examples. Alternatively, you may install the Firefox SQLite browser plugin described below.

Mac OS X

Bash

The default shell in all versions of Mac OS X is bash, so no need to install anything. You access bash from the Terminal (found in /Applications/Utilities). You may want to keep Terminal in your dock for this workshop.

Editor

We recommend Text Wrangler or Sublime Text. In a pinch, you can use nano, which should be pre-installed.

Git

Installing Git may require you to first install XCode. This is a very large download (several gigabytes), so please do it before arriving at the bootcamp.

For Mac OS X 10.7 and higher:

Go to the Xcode website. Get XCode from the App Store making certain to install the command line tools (from the Download preferences pane). Git is included in the command line tools.

For Mac OS X 10.6

If you have Mac OS X 10.6, first get XCode by going to the Apple developer site. You have to sign in with an Apple ID linked to a Developer account. If you don't have one, you can register and create one. Once you log in, go to page 8 and find "XCode 3.2.6 and iOS SDK 4.3 for Snow Leopard". Click to open that section, and then download the .dmg file. Finally, install just git.

Or, if you prefer a GUI, install Git for Mac by download and running the installer.

Python

Download and install Anaconda CE.
Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

SQLite

sqlite3 comes pre-installed on Mac OS X. Alternatively, you may install the Firefox SQLite browser plugin described below.

Linux

Bash

The default shell is usually bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.

Git

If Git is not already available on your machine you can try to install it via your distro's package manager (e.g. apt-get).

Editor

Kate is one option for Linux users. In a pinch, you can use nano, which should be pre-installed.

SQLite

sqlite3 comes pre-installed on Linux. Alternatively, you may install the Firefox SQLite browser plugin described below.

Python

We recommend the all-in-one scientific Python installer Anaconda. (Installation requires using the shell and if you aren't comfortable doing the installation yourself just download the installer and we'll help you at the boot camp.)

Download the installer that matches your operating system and save it in your home folder.
Open a terminal window.
Type
```
bash Anaconda-
```
and then press tab. The name of the file you just downloaded should appear.
Press enter. You will follow the text-only prompts. When there is a colon at the bottom of the screen press the down arrow to move down through the text. Type yes and press enter to approve the license. Press enter to approve the default location for the files. Type yes and press enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).

Miscellaneous

Firefox SQLite Plugin

Instead of using sqlite3 from the command line, you may use this plugin for Firefox instead. To install it:

Start Firefox.
Go to the plugin homepage.
Click the "Add Now" button.
Click "Install Now" on the dialog that appears after the download completes.
Restart Firefox when prompted.
Select "SQLite Manager" from the "Tools" menu.

Virtual Machine

Some instructors prefer to have learners use a virtual machine (VM) rather than install software on their own computers. If your instructors have chosen to do this, please:

Install VirtualBox.
Download our VM image. Warning: this file is 1.7 GByte, so please download it before coming to your bootcamp.
Load the VM into VirtualBox by selecting "Import Appliance" and loading the .ova file.