Tag Archives: brainstorming

Stuff for Alex to do this week


  • meet with me to talk about the plan for the week


  • create starter culture of e. coli
  • come to my talk at 1:15pm in the SUB (Santa Ana B, I believe)


  • do 1:10 dilution of starter culture in DI water, DDW, and 33% D2O)
  • take hourly time points of growth
  • help me work on #Scifund video (I’ll story board it on Tuesday after my talk)

I feel like I had more to say, but I can’t remember. Regardless if I can think of anything else, I’ll add it in the comments. Otherwise, let’s get excited, this is the beginning of a kickass summer of research!

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.

My #SciFund Proposal (a work in progress)

I just wanted to get this up today. Here is my #SciFund proposal on Google Docs. It is publicly open for comments. I won’t have a rough draft done until later today or early tomorrow so be sure to check back frequently. But in the spirit of open notebook science, I figured everyone deserves a chance to see the evolution in real time.

DDW Effects on Microorganisms

#SciFund Proposal Planning

DDW Project Proposal

Here is the link to my project proposal for the SciFund Challenge. There is nothing there yet, but I’ll fill it up tomorrow and Friday. The video stuff won’t come until next week and images will come after that. Right now I’ll be planning everything out, but first I’m going to do a bit of research. I’m going to read all the SciFund challenges from last year and pick out pieces that seem to really work as compared to how successful they were in their funding goals. I’ll write up a notebook entry on this later tonight.

In the meantime feel free to provide some helpful tips in the comments below.

#SciFund Challenge… I’m in!

I’m super excited because I just received word that I have been accepted to round 2 of the #SciFund challenge. I posted my pre-proposal last week, and from the looks of it I have a lot to do. I received an email that details what needs to be done this week and over the course of the month and some awesome details about the challenge:

  • 140 other researchers got accepted and we’ll all be working together to refine our proposals to make our funding goals. This is going to be a community experience all around: proposal editing will be a collaborative process, and the funding process is crowd based (hence crowdfunding). I’m very much looking forward to this experience.
  • This week my plan is to get familiar with the crowdfunding process and to develop my project proposal. I’ll be developing this in the open as usual so I’ll welcome all your feedback.
  • Next week and the week after, the plan will be to receive feedback for the proposal from others in the competition and hopefully all you who follow my notebook.
  • I’ll also need to develop a promotion strategy. That’s where the world comes in. I’ll obviously be tapping my family’s network, but I’ll also be asking you to tweet, facebook, +1 my efforts to help me reach my goals. I’ll also to to figure out how to get  the university involved and maybe take out an ad in the local newspaper to reach my goal.
  • At some point I’ll need to make a video proposal. So I’ll be needing some feedback on this. While I have video making chops and tools, this project will be the most important thing I do until I graduate so it will have to represent my best work. Anyone interested in helping me story board my proposal should comment below. Again, all that will be open.
  • Finally, I’ll need to come up with a reward program for contributors. This should be fun since I have a multitude of talents that I love to share with all. As an example if anyone contributes $100 I will design business cards for them for free (the printing cost is on the contributor). For a lower level contribution something like for every person who donates $15-25 I will email them a picture of Trex and myself doing experiments in the lab.
  • Finally between this week and next I will need to complete the first draft of my project proposal. According to the welcome email, “This first draft will include the following elements: title, video, rewards, images, and description of your project. Your project description should include the following: a welcome, a call to action, a detailed description of your plans, and a thank you. Please note that the project description should not go on for too long.” I don’t think I’ll be able to have a video done this week, but a story board should not be out of the question. I will look to film it next week.

That’s all for now. Like I said in the coming days, I’ll be setting up a Google Doc to outline and refine my project description, video storyboard, and reward system. Perhaps I’ll mindmap an outline. And remember all of this will be done in the open along with the project as it progresses once the funding is underway and complete! Crowdfunded open science? Yea, that’s awesome!

Project planning notes via Handrite

Here are some notes I took using handrite for android regarding my project plans. I don’t mean to advertise for anything, but I use this app ALL THE TIME and it is super helpful. Typing on my phone is annoying sometimes and Handrite allows me to use my finger to write (albeit sloppily). These notes were taken yesterday while I was meeting with Steve (on my phone) and now I have time to paste them in my notebook. So here is some background on my ramblings:

  • I would like to effectively analyze the amount of hydrogen-deuterium exchange in my samples. This is a phenomenon I’ve talked about a lot, know very little about, and stress a lot over. We tried FT-IR of water samples to see if we can determine differences in the water types. We’ve had mixed results in this regard. It boils down to the fact, that I don’t trust anything. How do I know that deuterium isn’t sneaking into my unopened bottles of DDW, or that hydrogen isn’t getting into my D2O? What about after it’s been opened? What about in my samples? If I’m going to get reliable results with yeast and e. coli I’ll need to know if I can trust commercial products.
  • NMR (nuclear magnetic resonance) seems to be a promising route to try and there may be some equipment either in the Chemistry department or Biomedical Engineering here at UNM that I’ll need to look into.
  • Mass spectrometry may be another avenue to determine precise amounts of deuterium in water.
  • Something not written but that I talked with Steve about yesterday and just remembered is that I need to talk with Sigma to find out how they measure the purity of the DDW and how reliable those measurements are long term. If something sits on a shelf for a year, how do I know it isn’t really just pure natural water?
  • I also have some stuff in my notes about the Repeating Crumley experiment. I just setup a D2O only experiment to show definitively that tobacco seeds do not grow in D2O. Previously I would only track this data for 10-15 days and Crumley went up to a month (if I remember correctly). I’ll write the setup in a minute, but I want to do 30 days so I have some pictures for my open access, self published RC paper (spoiler alert!).
  • Also to show that I’m no slouch, I want to try and repeat Crumley’s original experiment with paper towels to show that the growth of the 100% D2O seeds was due to H-D exchange and other environmental factors and not because they eventually grow in D2O. Yea I’m a badass.
  • The rest of the notes are some ramblings that are not really private but thoughts I would prefer not to elaborate on now.

Tata for now!

#SciFund Challenge Accepted!

If you watch “How I Met Your Mother” you’ll get the title of this post. But if you don’t then I’ll let it be known that I have just completed my submission for the second #SciFund challenge which is hosted by RocketHub.com. Here is my submission:

Effects of DDW on Microorganisms