The Third Bit

Science 2.0: the Future of Online Tools for Scientists

September 4, 2008 – 2:48 pm

A pub night and panel with Timo Hannay, Cameron Neylon, and Michael Nielsen, hosted by Nature Network Toronto

What does the future hold for the way we do science? Are online repositories such as GenBank and the physics preprint ArXiv, or social tools such as Nature Network, about to change science profoundly? To find out, join Nature Network Toronto for an interactive panel discussion over drinks at the pub.

Date: Sunday September 7 at 7:30pm

Place: Fionn MacCool’s (181 University Avenue, near corner with Adelaide)

About the panelists:

Timo Hannay is Publishing Director of Nature.com at the Nature Publishing Group, publishers of Nature and over seventy other scientific journals, plus numerous online resources for scientists. He is responsible for new online initiatives in social software, databases and audio-visual content. Timo trained as a neurophysiologist at the University of Oxford and worked as a journalist and a management consultant before becoming a publisher.

Cameron Neylon is a biophysicist working in molecular biology, biophysics, and high throughput methods. He has a joint appointment as a Lecturer in Combinatorial Chemistry at the University of Southampton and as a Senior Scientist in Biomolecular Sciences at the ISIS Pulsed Neutron and Muon Facility. He is developing an electronic notebook for biochemistry labs which has lead to his involvement in the Open Research movement and to his group moving to an Open Notebook.

Michael Nielsen is a writer living just outside Toronto, Canada. He is currently working on a book about The Future of Science. One of the pioneers of quantum computation, he coauthored the standard text on quantum computation that is the most highly cited physics publication of the last 25 years. He is the author of more than fifty scientific papers, including invited contributions to Nature and Scientific American.

For more information visit Nature Network Toronto (http://network.nature.com/group/toronto), or contact Eva Amsen (eva.amsen@gmail.com) or Jen Dodd (jen@jendodd.com, 519 572 2275).

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Rails Reviewer Wanted

September 1, 2008 – 6:44 am

For the past few days, Blake Winton has been reviewing every single commit made by a team of students who building a medium-sized Django application. We’d really like to find someone (not necessarily in the Toronto area, but that would make it easier for me to buy her/him lunch) who’d be willing to do the same for a RubyOnRails project that Prof. Karen Reid is running. As well as generally making the world a better place, it would also be a great way to meet (and recruit) some of our most talented students.  If you’re interested, please drop me a line.

Meanwhile, we’re teaching our daughter a new verse to an old song:

The zombies on the bus go, “Brains… brains… brains…”

Parenthood turns out to be fun in all sorts of unanticipated ways

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Mozilla Developer Days in Toronto Sept 15-16 2008

August 31, 2008 – 9:53 am

Via David Humphrey: a two-day workshop on developing for and with Mozilla will be held at Seneca College in Toronto on September 15-16, 2008.  The first day is meant for non-Mozilla devs who want to see how they can leverage the platform, contribute, or otherwise learn about Mozilla tech for their projects; the second day is more for current Moz devs and is focused on testing strategies.  The event is free, and people can sign-up at https://wiki.mozilla.org/DeveloperDays/TorontoSept2008.

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Community-Authored Books

August 26, 2008 – 2:30 pm

Via Michael Nygard:

O’Reilly is creating a new line of “community-authored” books. One of them is called “97 Thing Every Software Architect Should Know”… All of the “97 Things” books will be created by wiki, with the best entries being selected from all the wiki contributions.

The whole wiki makes for interesting (if uneven) reading.

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Summer’s End

August 26, 2008 – 2:20 pm

The last of our summer students finishes at the end of this week; here’s a few links to close off another great season:

• Dan Servos has finished his grade statistics visualization plugin for Moodle.
• Victoria Mui has been having fun with springs — her screencast is here.
• Eva Wong wishes she had a time machine (but had fun nevertheless).
• Matthew Basset thinks voiceovers are hard.
• Liz Blankenship has been thinking about simplifying tickets (a mockup is available); she has also posted some musings about the divergent evolution of Trac and DrProject.
• Qiyu Zhu has posted a screencast of the new-and-improved administration interface.
• Jeff Balogh says “thanks for all the fish” to his drag-and-drop form editor.

Thanks again, everyone — I really enjoyed working with you all.

(photo courtesy of Qiyu Zhu)

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A Pile o’ Links

August 26, 2008 – 7:13 am

Accumulated while on holiday—funny how sometimes I used this blog as an external strap-on memory pack.

• There’s a workshop on “Infrastructure for Research in Collaborative Software Engineering” atFSE in Atlanta this November.  Its aim is “…sharing experiences in evaluating and using open-source, academic, and commercial choices to conduct research, showcase how choices helped accelerate their work, and identify areas for improvement.”
• Emma Jane Hogbin had a few things to say at OSCON this year about women in open source.
• The winner of the 26th Annual Bulwer-Lytton Contest (for best bad opening line) has been announced. My favorite is still a non-winner from the early 1990s: “His eyes were cold and hard, which made them exceptionally difficult to chew.”
• A genetic map of Europe.
• A new CMS for building class websites, cool in part because its creator is 15 years old.
• Toronto Tech Week is Sept 22-26.
• The Linux Foundation has published a guide to kernel development that makes a nice companion to Karl Fogel’s Producing Open Source Software.
• Lambda the Ultimate discusses Ronad Loui’s “In Praise of Scripting” (freely readable draft here).
• Ontario’s Privacy Commissioner is hosting a one-day conference for high school and university students about how much of your life (not) to put online. See also the Chronicle of Higher Education’s article “When Professors Create Social Networks for Classes, Some Students See a ‘Creepy Treehouse’“.
• And finally, a latte printer you can make at home.

More later, including final wrap-up on Google Summer of Code projects.

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Bil Lewis Works With Biologists…

August 22, 2008 – 7:56 pm

…and occasionally finds it frustrating.

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Married

August 22, 2008 – 5:22 pm

Pictures say it better than words ever could:

Maddie in the Back Yard

Feeding the Fish with Mummy and Grampa

In the Big Chair

On the Beach

Sadie Looks Good in Hats

The Bride Makes Her Entrance

Love, Honor…

Cutting the Cake

The Sopranos Version

Families Together

Three Mothers

Uh, What Just Happened?

Posted in Family | 9 Comments »

Data Provenance Challenge

August 13, 2008 – 9:48 am

John’s summary of our discussion about what to teach scientists about reproducible research if they already believe it’s a good thing, and want to start doing it reminded me that I never posted about the Provenance Challenge. It has been run twice so far; each time, authors of tools to track the provenance (or lineage) of scientific data have to implemented some workflows, then answers questions about where data came from, what was done to it, and so on.  The results of the first challenge are described system-by-system in these papers (sorry, but it’s behind a wall — if you google for combinations of the authors’ names, you can find PDF preprints).  This is a very cool research area, and I hope one of my incoming grad students will want to do something with it.

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Winter Grad Course Evaluation

August 12, 2008 – 1:49 pm

I finally got a summary of graduate students feedback on the consulting course I ran this past winter. It was pretty good overall—on a scale of 1-5, the responses were:

How much background is required to successfully complete this course?	None	Lots	2.6
How easy was it to obtain details/background needed to supplement the lecture material?	Easy	Hard	2.7
Did the term work increase your understanding of the material?	Not at all	Very much	4.3
The material was presented:	Too slowly	Too fast	3.0
The material was:	Too broad	Too specialized	2.8
Was the workload:	Too light	Too heavy	3.5
How well organized or prepared was the lecturer?	Not at all	Very	4.0
How satisfied were you with the lecturer?	Not at all	Very	4.7
Overall rating of the course	Bad	Great	4.5
What resources did you use heavily for the course?		Lectures	2
		Text	0
		Papers	4
		Reference Books	0
		Course Notes	0
		Friends	2
		Lecturer	2
		TA	0
		Internet	10

Advice to people who are considering the course in the future:

• If there’s a project you’re interested in or something you want to learn, this is a great way to spend time doing it and getting a course credit at the same time.
• Great course. Find a good project and give ‘er.
• This course is what you make of it. You can mold the course in order to get out more of what you are interested in. I found this freedom great!
• Lots of projects to choose from.
• Good if you want some public speaking experience.
• This course is very good for undergraduate students. It will enhance their coding skills and give them a good opportunity to find a job (by linking them to people in industry). If you are a graduate student and your thesis involves building an application, it’s a very good chance to pass a course as you are doing so.
• Great course. You will learn a lot, but make sure you make realistic estimates of how long everything will take, otherwise it will be too much work.

General Comments — Good

• Provides great insight into large project development.
• Lecturer was outstanding!
• Interesting discussions.
• You can do many different things (develop applications) in this course.
• Learn a lot; things you won’t learn in any other course.
• Hands-on learning and real-world experience.

General Comments — Bad

• Very code intensive, not very appropriate for grad students if the project is irrelevant to their research.

I’m now looking for project ideas for students in the fall — if you’re interested, please drop me a line.

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