Tag Archives: publications

A cool figure I forgot to share: E. Coli growth in Water

the e.coli data reimagined in illustrator

I made this figure for my rockethub proposal and forgot to post it here in my notebook. Look how pretty it is!

I made this in Adobe Illustrator and if anyone is interested I would be willing to host an online workshop to teach others how to use Illustrator for science. This particular image took almost no time (maybe 30 minutes), which is a marvel because I obsess over everything I do in Illustrator (which is why there isn’t anything tangibly Illustrator on this site).

IGERT Limited Competition Results

I just received word that the UNM limited competition results are in. Our IGERT proposal has been selected by UNM to proceed to the NSF letter of intent phase! That’s great news! Open science is finally being recognized by UNM as a major innovation and key for scientific development and they are going to help us push this forward to the NSF.

The letter of intent is due June 4. Any feedback I receive from the limited competition committee will be posted online.

In the meantime follow the next phase on the document which can be found here.

The Open IGERT Proposal

I’ve been saying for months that I want to submit a proposal to the NSF for an open science IGERT. Well the call for such a proposal dropped into my lab a week ago and UNM is doing a limited competition to pick the best proposal to send into the NSF.

Since I’m an open notebook scientist and everything, I’m going to write this proposal openly despite my actual fears about doing so. Because it’s best to be open!

Some key aspects of the proposal are that the NSF is looking to train students in the ways of data management and to do science in the 21st century. So I’m pairing with UNM Library Scientist Rob Olendorf to design an open science repository for UNM students (for data, blogs, notebooks, etc) and we are going to train students on modern data management techniques and how to do science openly, online.

Right now, these thoughts are still being hashed out but you can see the progress we’re making in this document:

IGERT Proposal

And if you haven’t checked out my rockethub project please do so!

Shameful self promotion

Everyone always says shameless, so I’m going to begrudgingly promote myself and do it very shamefully (in case you can’t be full of shame and be grudged).

Anyways, a couple weeks ago Mark Hahnel asked me if I had any kind words to say about figshare, and if I did would I mind speaking them aloud. I said sure, and then proceeded to talk to the empty lab about how great figshare was. I reported back the results of the empty conversation, and Mark explained that he meant that I write a post about them for the SoapBox Science Blog over at Nature.

So I got in touch with Laura Wheeler, and I started a Google Doc so she could real-time review my post. I wrote and she told me it was all wrong (actually she was very supportive!) and I wrote some more. The real-time collaboration would have been awesome if I didn’t go days between edits. But nonetheless, eventually the post was finished and she published it to SoapBox Science. Here is the link:

Woohoo! I’m published in Nature bitches!

And so that completes my story. I regretfully inform you that my boasting did not fill me with joy in the slightest bit, and I wish I hadn’t even mentioned this post at all. Nor do I wish I had mentioned it on Twitter a couple times, and I especially wish no one had tweeted my story either. But what’s done is done, and I can’t change the past, nor can I tell people to stop doing it in the future. I’ll just have to live with the repercussions.

Take that UNM administration who thinks that online science is useless, and see no merit or value in open science.

Again I apologize for burdening you with the post…

Sincerely,

IhateAnthony, do you?

My NMGPSC Presentation: “Open Notebook Science: Research in Real-Time”

I have to say, this is quite beautiful and hopefully informative. The talk is scheduled for 15min and I plan on moving through the slides quickly. I’ll practice in the morning and time it out to make sure it fits in the scheduled time.

Presentation: “Open Notebook Science: Research in Real-Time” – Slideshow Outline

Here is my slideshow outline. This is basically the framework for what I’m going to talk about without images and fancy text. You know me. I gotta make it pretty…

Open Notebook Science: Research in Real Time

Presentation: “Open Notebook Science: Research in Real-Time” – Script

Yesterday I wrote up an outline for this presentation and now I’m going to write up a basic script so I know what I want to design my slides around. I ended that post by starting this one:

I think I want to start the talk by projecting a hypothetical future. In this future, peer review  publications are either non-existent as we currently know it, or they are reserved for organizing information scattered across notebooks. I will talk about a future where scientists get information directly from other labs, instead of peer review articles. Research is updated in real-time and scientists have full access to step-by-step protocols, raw data, software and code, thoughts, notes, ideas, and anything that may come up during the scientific process.

That future is beginning now and it’s starting with open notebook science.

I think I still want to begin there, but I also wrote that I wanted to include tools of the trade, and I’m thinking that doesn’t fit so well into the talk. Instead maybe I can present tools of the trade through the examples I wish to demonstrate (my notebook would highlight successes, sharing, wordpress, figshare, benchfly, etc). In any case I’ll get into a writing zone and then see if it makes sense to include that information. Let’s get to it…

The internet has brought about radical changes to the way that we all interact with the world around us. In academia, knowledge is spread at an exponential rate thanks to social media and the people willing to share their ideas with the world. Recently, the open science movement has brought about tools that allow researchers the opportunity to host and publish their data and methods to bring similar changes to the scientific community.

Traditionally scientific information is shared through peer-reviewed journal articles. Researchers spend a great deal of time formatting their methods and data to conform to the editorial process and then spend even more time trying to get their data through the peer-review process. While the intent is good, peer-review which is intended to weed out erroneous information ends up as a major time consuming portion of the publication process. In the end, even faulty or completely erroneous data will eventually get published. And thanks to Google, that data is just as likely to be discovered as much more credible information.

Open notebook science is the next generation of scientific publishing. By maintaining an open notebook scientists keep a detailed account of ideas, methods, data, and results providing a full transcript of an experiment through the entire scientific process. Ideally this record will be kept in real-time allowing collaborators the opportunity to access scientific data directly from a lab as the experiments take place instead of waiting 6 months or longer for the information to be published traditionally.

I treat my open notebook as an ideal system and maintain every aspect of a given experiment. My notebook is hosted on my own website (IheartAnthony) and uses the WordPress platform because it is open sourced and there is already quite a large and developed infrastructure and community.

From my notebook, you can access experiments from initial ideas all the way through to the final results. The information is search engine indexed so others can easily access information that may relate to projects they are working on. Also, by going open, I’ve bridged the gap between taxpayers and funding agencies and the labs that they fund.

(Show examples of the notebook)

Also by using wordpress I’ve built a system that allows me to incorporate other web tools to host scientific information. I can use videos through BenchFly and Youtube to host video protocols, I can host images to detail projects, I can embed cloud word processing (Google Docs) to keep real-time data and share it, and I can use commenting systems like Disqus to engage the community both public and scientific to give my notebook life. This also allows for my notebook to be peer-reviewed in real-time.

The major issue right now is that the open science movement is relatively new and open notebook science doesn’t have many practitioners (show wikipedia article). As such the community of engagement is quite small but extremely diverse. In order to show the effectiveness of ons in a real-world environment I built an open notebook science community in the Physics 308 Electronics Junior Lab that I’m teaching.

Students in the lab were given some initial conditions and were allowed complete freedom otherwise to demonstrate an open scientific system.

Initially they were allowed to pick any online system that could be used to keep notes, but they were offered the suggestions of using Google Docs, the Github wiki, and WordPress. The students picked the platform of their choice and the amount of students representing each platform is pretty uniform.

They were taught the principles of ons: keep a detailed record of your data, clearly write methods, and try to maintain some semblance of organization. Posting more is much better than posting less or worse, nothing at all. In that sense, students were encouraged to post whatever they wanted in their notebooks, because even wrong information could be benefitted from.

The students were also required to collaborate and communicate with one another. Each platform has some form of commenting system built in, and students were encouraged (and required) to read each others notebooks and provide some weekly feedback.

The final rule was that students were allowed to “cheat.” By this I mean, they were allowed to use each other’s software code, they were allowed to find the answers to problems in each others’ notebooks, and they were allowed to Google anything they didn’t understand or couldn’t figure out. By allowing them to do this, we’ve allowed them to perform exactly as they would in the real world.

So in effect, the class became an experiment in open notebook science, which turned out to be pretty successful. (Illustrate successes)

End with details of benefits of ONS.

 

 

Presentation: “Open Notebook Science: Research in Real-Time” – Outline

I changed the name of my talk on Tuesday from “Open Notebook Science” to “Open Notebook Science: Research in Real-Time.” I figured most students wouldn’t know or care about open notebook science on it’s own, so I added the extra bit to highlight the one aspect of ons that makes people say “That’s so cool!” when I talk about it. I still have a ton of work to do for this talk, but here I’m going to write up an outline and then tomorrow I’ll throw together some slides.

I’m still debating on how to present. I’m a huge fan of mindmeister for presentations, and it could be high impact on the audience, but I’m worried about internet access and website loading times. I can’t believe that is something I have to worry about nowadays. Regardless, I think I’m going to have to stick with PowerPoint, well I’ll be using LibreOffice which is open sourced software and I think is an extension of OpenOffice.

Anyways here is my outline:

  1. Basics of ONS
    1. values of ons
      1. research in real time
      2. instant collaboration
      3. access to scientific information from project intialization to completion
        1. project ideas/planning
        2. protocols/methods
        3. data (raw and formatted)
        4. conclusions
      4. alternative publishing
  2. Tools for ONS
    1. host
      1. wiki
      2. cms
        1. wordpress
        2. drupal
        3. joomla
        4. blogging platforms
      3. google docs
      4. if you can add multiple content formats, it can be a notebook
    2. supporting software
      1. youtube/vimeo/bencfly
      2. flickr/picasa/etc
      3. figshare
      4. disqus/commenting system
      5. phone apps
      6. anything in the cloud that can be embedded!
  3. ONS Community – Physics 308L Junior Lab
    1. students allowed to choose notebook system of their choice
      1. github wiki
      2. google docs
      3. custom wordpress site via IheartAnthony
    2. rules
      1. must notebook everything
        1. be clear, detailed, and organized
      2. must communicate weekly
        1. read everyone’s notebooks
        2. comment in other notebooks what you like/how to improve notebook or technique
      3. allowed to “cheat”
        1. students in wednesday lab could read the monday labs and use their notes/software/methods etc
        2. allowed to surf internet for better tools, software, etc.

I would like to focus more on the benefits of ONS and the success of the lab than I would on building an open notebook. One of the reasons is because building and maintaining an open notebook is a much longer discussion and I would rather it be a discussion than talking at people. For that reason I may give a workshop this summer for students interested in keeping an open notebook.

The other reason is because my goals for this short talk (15 min or less) is that:

  • I want to raise awareness of open notebook science (as many students are unfamiliar with it, even in principle)
  • I want to show the benefits of ons over traditional note taking and over traditional publication
  • and I want to show how a collaborative community would behave, and this is what the lab simulates.

I think I want to start the talk by projecting a hypothetical future. In this future, peer review  publications are either non-existent as we currently know it, or they are reserved for organizing information scattered across notebooks. I will talk about a future where scientists get information directly from other labs, instead of peer review articles. Research is updated in real-time and scientists have full access to step-by-step protocols, raw data, software and code, thoughts, notes, ideas, and anything that may come up during the scientific process.

That future is beginning now and it’s starting with open notebook science.

How does that sound?

Tomorrow I’ll post what I imagine I’m going to say and my first (and possibly last) draft of the talk that I’ll be giving.

SACNAS Conference Poster

As part of my contribution to my newly appointed fellowship in the IMSD program here at UNM, I am required to attend the National SACNAS Conference which is to be held in Seattle. I’ve decided to present a poster as opposed to giving a talk because it will allow me to talk more freely with students who may be interested in the millions of questions there are about open  notebook science. Here is the abstract I submitted:


Open Notebook Science: Tools of the Trade