Archive for November, 2011

Particle-Surface Pendulum

Here is an actual picture of the pendulum and a movie of it in action.

Photo of the particle-surface pendulum
Figure 1: Photo of the particle-surface pendulum. This is a photograph of the pendulum designed in a previous post. As you can see, there is a protractor that marks the angle at which the pendulum is raised.

Here is some calibration data taken by a new undergraduate to the lab, Sarah D. Labianca.

Here is a movie of it in action.

open notebook science logo

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Particle-Surface Interactions Pendulum

My new boss, Hugh Smyth, has given me the green light to do open notebook science on some of the projects I’m working on in the lab. The project I’ll discuss below is especially cool since it is simple and relatively straight forward to accomplish. Plus, the fact that Hugh is excited about open notebook science makes it all the more fun.

What I designed is a very simple pendulum that has the capability to whack the heck out of something. Figure 1 is a SketchUp image of the pendulum showing the basic design.

SketchUp image of a pendulum design using parts from Thorlabs, McMaster-Carr, and Precision Balls.
Figure 1: Particle-Surface Pendulum. Thorlabs parts were used as the structure. There is a double sealed ball bearing that allows the stainless steel ball to swing freely. The item to be whacked is placed in the optics holder. The SS ball came from Precision Balls and all other items came from McMaster-Carr.

It works surprisingly well and I’m happy about its design. There are a few issues with it that I will discuss when I post real images of the build. Till then, here is a parts list for, what I’m calling the “Pendulum 5000″.

Parts List

Thorlabs
McMaster-Carr
  • 92311A535 – 1/4″-20 Set Screws.
  • 7804K143 – Flanged Double Shielded Ball Bearing.
  • 92185A535 – SS 1/4″-20 Socket head cap screw 3/8″.
  • 8517A58 – Stainless Steel Protractor.
Precision Balls

As a final note, getting Figure 1 to display properly was a heck of a feat due to my lack of HTML skills. So, I’m going to post the code for it below. The reason why I didn’t use the built-in WordPress figure + caption gui is that it wouldn’t allow me to bold or italicize words in the caption. So, I had to build a table to stick the figure in. Even posting the below code was a pain since the symbols < and > are rendered as HTML tags and need to be escaped with their ASCII equivalents.

<div id="image" style="width: 330; margin:0 auto; background: lightgray;">
 <table class="image">
  <tbody>
   <tr>
    <td align="center"><a href="http://image"><img class="size-medium wp-image-20" title="" src="http://image" alt="" width="300" height="200" /></a></td>
   </tr>
   <tr>
    <td class="caption" align="left"><strong>Figure 1:</strong> <em>Title</em>. Caption</td>
   </tr>
  </tbody>
 </table>
</div>

open notebook science logo

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ONS logo

It would be nice to have a way to track all the open notebooks out there and it was suggested by Bill Hooker that those of use using open notebooks to put a logo by Jean-Claude Bradley on the webpage that the notebook is on. This is a great idea and one that posses a very interesting challenge: if ONS scientists use the logo, how do you crawl the web to find the logo so that you can curate the notebook?

At any rate, any of my notebook entries about with ONS in it will now have a logo associated with it. I’m putting “open notebook science logo” as the alternative text in hopes that maybe this can be tracked somehow.

open notebook science logo

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Open Science Article Repost

Michael Nielsen gave a great interview about open science. There are a bunch of links to interesting tools available for the open scientist that I should definitely look into. He even gave me and Steve Koch a nod.

http://scienceblogs.com/confessions/2011/11/interview_with_michael_nielsen.php

I must admit that I find it overwhelming to see all the different tools that keep popping up everywhere that can be used for open science. This is a good and a bad thing in my mind. Good because it allows one to choose the method that they want to use in order to do some open science, and bad because there is no standard way of dealing with open notebook science and no unified repository where we can place our open notebooks, or even link to them. At some point in time I suppose this will change.

Even though open science is in its infancy, we still need to start thinking about how best to archive and advertise that a scientist is doing open science. And, as Michael’s interview suggests, there are starting to be a lot of people wanting to cater to open scientists. I think it’s now up to the open scientists to start talking to the sites that are attempting to offer us the tools we need to tell them exactly what we need and how best to serve open notebook science. After all, communication is the backbone of open science, why not start to communicate to the developers what we as open scientists need the tools to look/function like?

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Open notebook science

Crawled open notebook science

Yesterday, I did a Google search for a procedure I developed in grad school on OpenWetWare, my former open notebook where all my original content was placed. In the search results, I came across a website that had crawled my notebook and reposted a page on their site. This website seems to be about AIDS research but, my original notebook entry has nothing to do about AIDS research. You can take a look at it here. While I have come across other blog type websites that repost my original content, this is the first I’ve seen of a “medical” website reposting my content.

This website is obviously a site that is culling content from other places on the web. The science I did was completely unrelated to any forms of human health research. It was basic research, research done on a fundamental level with zero clinical implications. What happens to the people that are searching the internet for information on a scary subject such as AIDS and they come across my content there? Now, I’m happy that in the future, sites that crawl and repost information will help to perpetuate my original content. However, the information is now on a site guised to be about information on a deadly human disease. What if the person reading it does not possess enough information to filter my post and realize that it has zero pertinence to them? As a scientist and an educator, this concerns me a lot.

The persistence of ONS

It would seem that the persistence of original content in open notebook science will continue through repostings, however, without context to the content, that science is useless. This is not a good thing and has the capability of destroying the science being done in open science. I have no clue on how to fix it and this should be discussed at ScienceOnline2012 of which, I need to remember to register for.

Now, the origninal reason why I decided to start a new notebook on WordPress.com was because there are implications about using a service that has not been proven to be externally funded. For instance, what happens when the service is no longer available and all your content is gone? Of course, there are services such as the WayBackMachine that attempts to archive webpages but, from what I understand, services such as this are not well known and are basically an “after-thought” and an “exercise for a librarian” in the scientist’s mind.

Also, as gruesome as it sounds, I will eventually die. What happens to my scientific research then? Doing simple searches for some of the most popular sites around (in this era) on what to do when a user is deceased and how to access/memorialize their accounts shows that there is no standard procedure on the subject. If you have your own server and are using it to post your open notebook science, what happens to your content when you are no longer able to pay the fees associated with owning a domain? From what I understand, unless it has been archived, poof – it’s gone. This is not a good thing since open notebook science is a treasure trove of data; not only for science in the present, but for future historians and other scientists. It’s even a giant data source for linguists of the future because I’ll bet you $1 (which will probably vest to a lot of money in the future) that the language we speak and write now will not be the same in 500 years.

Both scenarios, culled content posted on unrelated websites and vanishing open notebook science due to death/lack of funds, are things that need to be discussed. Open scientists need tools in order to keep the persistence of open notebook science alive. Does this mean creating a non-profit to house our data or does it mean that University Libraries need to create programs in order to archive ONS?

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