If you are planning to go to the PHYSOR 2012 meeting in Knoxville, please consider helping Anthony Scopatz lead a Hacker Within session there. We've been invited to give a 4 hour workshop on scientific computing best practices.
>>> Successful THW@UT bootcamp
A post over at the software-carpentry website gives a rundown of the bootcamp recently taught there with help from THW. Check it out!
>>> Scientific Computing Tutorial at ANS
THW is flattered to have been invited to offer a super condensed version of its previous scientific computing bootcamps at the American Nuclear Society winter conference. This tutorial will be given as a part of the Young Professionals Congress, an embedded topical of the conference, which provides a forum for young nuclear professionals to address the challenges facing the next generation of nuclear professionals. This super-mini-course will be in a special demonstration format and will motivate the use of tools and skills appropriate for nuclear engineers. It will touch on topics such as developing, organizing, managing, and distributing software.
>>> Code Sandwiches
This Friday, 9/30/11, THW will meet in room 414 of the Engineering Research Building at 3:15pm. Steve Jackson, UW CS alumni and programmer in Paul Wilson's research group will be presenting.
>>> THW Presentation at ANS
In the education track at the American Nuclear Society annual meeting, Katy 'Southside' Huff gave a talk about the THW bootcamp model. The summary will be published in the ANS transactions. Follow the wiki support materials link for the presentation and summary.
>>> THW@MSU Bootcamp Sucess
A post over at MSU's high performance computing center website documents a greatly successful THW bootcamp. Check it out!
>>> THW@MSU Bootcamp Begins
The THW bootcamp at MSU will begin tomorrow, Saturday June 4th! Hackers Wolfman, Wokmage, and Southside are thrilled to be your faithful representatives, but you too can keep up with the proceedings on convore (convore.com/the-hacker-within-msu-2011), on twitter, and with irc ( #thwmsu ).
>>> Reproducible writing workflows: One file to rule them all
[RESCHEDULED] Friday, May 6th @ 3:15pm in ERB106. Do you have multiple copies of your paper (dissertation) labeled draft1, draft2_from-paul, pre-final, etc... When your paper comes back from review, does it take days to find all the pieces and remember which copy of your code is the latest? Do you dread converting your favorite format X, to your collaborator's favorite format Y? Can these predicaments be avoided with one text file, under version control? Nico Preston will lead the discussion and demonstrate a potential workflow.
>>> Why Present?
On April 15th, Nico Preston will lead "Why Present?" a discussion on academic presentation use cases and demonstration of tools for each. This "un-talk" will not include a slide deck and raises the question: do slides help the discussion? Instead, Nico will fat finger unfamiliar operating systems, and entertain with live code demos.
>>> Beamer
On Friday, April 1st, in ERB 106 at 3:15 pm, Eric "Wolfman" Howell will lead a discussion of Beamer, the system for making presentations with LaTeX. He'll discuss some tips and tricks for building presentations with beamer, as well as his experiments with some templates. There will be a chance for everyone with Beamer experience to share their own tips, tricks and templates as well, so if you're familiar with Beamer please come armed with hints for your peers.
>>> Cython
Aronne Merrelli will be presenting on Cython: C-extensions for Python, and what to use when you can't vectorize your algorithm." Python with NumPy is a very efficient and fast method for implementation of scientific computing algorithms. However, algorithms must be vectorized in order to take advantage of the fast NumPy array object, and vectorizing may be difficult or impossible in some cases. Cython is a language extension to Python which allows easy interface to existing C libraries and automatic conversion of code into compiled C modules. Cython implementations show huge speed advantages for non-vectorizable problems. He'll present test cases using Cython to generate fast compiled modules entirely from the Python interpreter, and compare these to pure Python and Python/NumPy implementations. See you tomorrow, Friday March 25th, at 3:15pm in ERB 106!
>>> LaTeX
The talk on Friday March 4th will be about LaTeX. It will cover the basics of what LaTeX is, how to get LaTeX, how to create a LaTeX document, and some tips and tricks for using LaTeX for scientific writing.
>>> inSCIght episode 1
The second episode (Episode 1) of the inSCIght podcast is available at inSCIght.org . This week's topic is Managing and Maintaining Legacy Code and the podcast this week stars two individuals you'll recognize as devoted providers of THW snacks.
>>> The Long and Winding Road Before int main()
This Friday (Feb. 18) Josh Danczyk will give a talk about processes. This talk is primarily concerned with what takes place before a program enters 'int main()'. Specifically, it deals with x86_64 Linux and compiled C code in an ELF format, though much of what takes place is general. Please join us at 3:15pm on Friday February 18th in room 106 of the Engineering Research Building.
>>> Perl Data Language
The first "Spring" THW meeting will be tomorrow, Friday Feb. 4th at 3:15. Importantly, this semester, we're going to try a new room. Though we'll still be in the engineering research building, we'll now be in room 106. This meeting will be led by Puneet Kishor who will discuss his applications of the Perl Data Language. Puneet is a researcher at the Forest Ecosystem and Ecology lab on campus and a Science Commons Fellow (evangelist of open science) in the broader world. The Perl Data Language will be particularly useful for those of you dealing with large datasets. Of course, if it is secretly Puneet's charming demeanor or the promise of Rachel's tasty snacks that draw you to the table, none will be the wiser.
>>> Software Carpentry Bootcamp Feedback
Thanks so much to those of you who came to the software carpentry bootcamp! If you like this sort of thing, please sign up for the listhost (http://groups.google.com/group/hacker-within). Finally, one of the myriad reasons that we donate our considerable efforts to events like this is that we hope to learn how to be better teachers. To help us, please click 'view wiki support materials' below to fill out the feedback form.
>>> Software Carpentry webcast
We will be webcasting the Software Carpentry Bootcamp through Evo (evo.caltech.edu). The meeting name is 'THW Software Carpentry Bootcamp.' This includes a Skype and phone audio bridge--for that fireside radio broadcast experience. Note: we will be archiving and hosting the webcasts. Please click 'wiki support materials' for details.
>>> Prepare For the Software Carpentry Bootcamp
Many thanks to those of you who have registered for the Software Carpentry Boot Camp. We're thrilled that there are so many of you! If you have registered, please do two things to prepare for Wednesday. First, download and install Virtual Box at virtualbox.org. Then, watch the lectures at software-carpentry.org covering the shell, version control, make, databases, and testing. For other suggestions read the wiki support materials for this post.
>>> THW Identi.ca group created.
Subscribe and post! http://identi.ca/group/thw
>>> Software Carpentry Bootcamp Registration Now Open!
We're thrilled to announce that registration is now open for The Hacker Within Software Carpentry Bootcamp! The bootcamp is a three day workshop on tools for scientific computing. We're delighted to announce that we'll be joined by Professor Greg Wilson of software-carpentry.org upon whose curriculum this course is based. The bootcamp will take place on January 12th, 13th, and 14th from 10:00 am to 3:30 pm in 1800 Engineering Hall. Registration is completely free, so please sign up at http://hackerwithin.org/thw/plugin_wiki/page/scbcRegistration .
>>> Welcome to our new website
This is our new website. We will be porting our archival content to this platform over the coming weeks. Please stay tuned ...
>>> Unit Testing
This Friday, December 10th, a Software Carpentry Beta Testing meeting will be led by Rachel Slaybaugh, a graduate student in the NEEP department. The topic of this tutorial will be Unit Testing. She'll lead exercises that walk us through developing our own unit tests. The meeting will be held in CAE 175 at 3:15 pm on Friday. Before you arrive, please prepare yourself for these exercises by checking out Greg Wilson's lectures on the topic at http://software-carpentry.org/4_0/test/.
>>> Stuart on Parallelization with Python
This Friday's meeting will be led by Stuart Slattery, a graduate student in the Nuclear Engineering and Engineering Physics department. The topic of his talk will be Parallel Programming with Python. He'll demonstrate quick parallelization tasks using python tools. As usual, the meeting will be held in ERB 414 at 3:15 pm on Friday.
>>> Professor Paul Wilson on XML
This week, Professor Paul P.H. Wilson will be sharing insights on input parsing with XML. This markup language is a versatile tool particularly useful for the representation of arbitrary data structures. It is therefore a strong tool of choice for development of sophisticated schemas with which to interpret user input parameters and data. As a recent thread reminded us (the most replied-to thread in THW history! ), there are myriad input parsing options appropriate for a range of our computational science workflows, so learning about one of them is likely to be very helpful. Also, there will be snacks!
>>> Web Programming
This Friday November 12th, Nico will be teaching web programming with the Web2Py framework (http://web2py.com/). We will be testing a new slide deck, so there is no preparation required. We're also trying out a different computer lab in the Enzyme Institute, 1710 University Avenue, room 208.
>>> John D. Hunter Invited Lecture
I'm excited to announce that Friday, November 5th, we'll be hosting a distinguished lecture from Dr. John D. Hunter, an accomplished computational scientist, open source programmer, and the author and lead developer of the pervasive python visualization library, Matplotlib. Dr. Hunter's talk is entitled "Matplotlib and the Python Ecosystem for Scientific Computing" and will be held in room 1106 of the Mechanical Engineering building at 2:00 pm on November 5th. This talk will be open to the whole campus, so please bring your colleagues and forward this invitation widely. This special event was cooked up by Matt "Spidr" McCormick who was assisted by your treasurer Matt "BlackBeard" Gidden. They together secured a grant from the UW Lectures Committee. Critical steps in this process were supported by both the Department of Medical Physics and the American Nuclear Society.
>>> Build Systems
The next Software Carpentry Bootcamp beta testing session will be Friday, October 29, at 3:15 in 175 CAE. Matt 'Spidr' McCormick will cover Build Systems. A build system can make your project configurable, create a Make system that speeds up development, and make it installable. We will go over what this means, why you want it, and hands-on examples for a C++ case and a Python case.
>>> Awesome Sauce With Tom and Richard
Young THW upstarts, Tom and Richard, will be presenting to the group some neat tools they have used over the years. They'll cover various Windows tools including Hamachi and CCleaner as well as Linux tools such as quick synergy and teamviewer. They'll also give a demonstration of the free and open source Mathematica alternative, Maxima.
>>> Automated Documentation
This Friday, October 15th, I, Katy Huff, will be giving the third in our series of tutorials on Software Carpentry. We'll meet this afternoon at 3:15 pm in CAE room 175 to try some hands-on examples of automated documentation. So, if you've ever wanted to learn how to effortlessly create a full suite of pdf, html, and .tex documents detailing the data structures and functions in your code please join us for this tutorial. Specifically, we'll be doing some examples with Doxygen, but Sphinx will receive some attention as well.
>>> Nico on web2py via Evo
The regular meeting tomorrow at 3:15 pm in ERB 414 will be a tutorial (via Evo) on web2Py by our very own Nico Preston. This will be the platform on which we rebuild the website, so if you have any desire to help us rebuild it over the next few months, this will be an important prerequisite.
>>> The Shell
This Friday, October 1st, a whole team of us will be giving the second of our series of tutorials on Software Carpentry . We'll meet Friday afternoon at 3:15 pm in CAE room 175 to try some hands-on examples of the Shell, so if you've ever wanted to learn some tips and tricks for operating a terminal, please join us for this essential tutorial. Finally, please review the brief lectures on Greg Wilson's Software Carpentry website prior to the meeting ( http://software-carpentry.org/blog/shell/), and don't hesitate to leave comments and questions. Hope to see you there!
>>> Wolfman’s thoughts on writing large sciencey documents.
This week our own Eric Howell will be sharing insights on the many tools he's used in his prelim, thesis, and general `sciencey' writing processes. His talk is entitled "Death to Clippy! Wolfman’s thoughts on writing large sciencey documents" and will certainly be full of gems that we can all use in our own computational science workflows. These include reference managers and the Wisconsin Thesis LaTeX template, so please don't hesitate to bring along friends and officemates who might be similarly interested. You many entice them with the promise of heavenly snacks.
>>> Version Control
Today we'll be giving the first of a series of tutorials on Software Carpentry topics. We'll meet this afternoon at 3:15 pm in CAE room 175 to try some hands-on examples of version control. If you don't have a CAE account, or would prefer to use your laptop, please bring it along. We'll be using python2.5 or better as well as the pygame library. If you have time to install those things before the meeting, please do. Please review the brief (and hilarious) lectures on Greg Wilson's Software Carpentry website (http://software-carpentry.org/blog/vc/) prior to the meeting.
>>> Saving Scholarship: Libraries and Digital Data
Dorothea Salo, Digital Repository Librarian at the University of Wisconsin, to discuss "Saving Scholarship: Libraries and Digital Data." In this talk she'll touch on the software and hardware challenges of digital data management and how these concerns affect researchers in the computational sciences.