Category Archives: Open Notebook

Small-ish issue with digital object identifiers

I’m no expert in this space, but I came across an issue with digital object identifiers because of my annoyingly persistent use (overuse? hahaha) of figshare. What happens if the archive tool you use for your data switches from one permanent link system to another?

Back in the early days of figshare, they used the handle system to provide a permanent link for data stored in their system. At some point they switched to using the DOI system. I have no idea when it happened and I don’t even think I noticed the change. The only thing I know now is that my older figshare datasets are full of dead links.

The point of using a permanent link, ie a handle or a DOI, is to maintain a connection to the source if the URL or data at that source changes. Any changes will result in a change to the metadata which will allow the permanent link to point to the correct location. This allows you to change the URL for a dataset on figshare, for instance, and the DOI link will point you to the updated location.

In my case old projects that were linked via the handle system are all updated with DOIs. Since the two systems are different, I have the unique situation of having broken permanent links! Obviously, this defeats the purpose of a permanent link. So it seems I have some work to do to find all the outdated figshare sets and update them, which presents a very tedious set of challenges.

Has anyone ever experienced anything like this? I’m not familiar with the internal workings of permanent link systems, but is there a way to easily move from one system to another? Does this present an issue for the future of web science where DOIs or handles are obsolete? I imagine in that world there would need to be a system wide effort to ensure everything is upgraded properly (like switching from paper to electronic records).

100% Real-time publication: an experiment in #opennotebookscience

I’ve long been an advocate of open notebook science. In my advocacy, I am always looking for new ways to encourage fellow researchers to pursue this methodology for their own research. The latest of which pertains to archival and citability.

The ability to receive credit for your research, has been a requirement of science culture for quite some time, and is presently essential to an academic career. The altmetrics movement has been a valuable way to track and receive academic credit for new and nontraditional publication methods. Online tools like Impactstory help to track these activities, while tools like Figshare help propagate data and track your online impact as well.

This has always been missing from open notebooks.

I’ve always advocated against the need for a singular open notebook platform for the reason that ONS needs to have the flexibility to meet the needs of the scientists who use it. I’ve also never actively pursued a tool that can provide that formal citation credit since there are APA, MLA, etc rules for citing websites and other online resources. But the success of Figshare and other software has made me rethink this approach.

If open notebooks could have an automatic way to apply either a handle or a DOI, and could be archived, I think people would pay attention. If there was a publishing platform that could freely contain all the information of an open notebook, give the notebook a DOI (for instance) for each entry, and then host the final publication for peer review, there would be an even bigger incentive for ONS. And obviously there would be more transparency in the research process.

Where am I going with this?

Well a few days ago, I did a search for “DOI for WordPress” and came up with this, a plugin for a website called The Winnower. I had never heard of this organization so I went to the website and found a world of opportunity.

The Winnower, in case you are unfamiliar, is self-labeled as a DIY science publication platform that features a post-publication peer-review process to expedite and lower the entry barrier for publication. Once you submit your manuscript you can request a DOI for your article, which will undergo changes as you receive feedback for the publication.

The aforementioned plugin allows you to post blog entries (self-hosted WordPress blogs only for now) to the Winnower and receive DOIs, and with it the easy ability to be cited, for those entries. Integration between an open notebook and the Winnower (or a platform like it) could be a huge step forward for the ONS movement.

Imagine being able to see the entire scientific record for a study contained in the same system. Even better, imagine being able to witness the development of the study in real-time, providing feedback to the experiment, and being active in its development. When it comes time for peer-review, the process should theoretically be quick, because the work should have been vetted. If it hasn’t already, then it is relatively easy to review the prior work summarized in the publication, because it is all self-contained on the publishing platform (or the open notebook where the publication is).

In the interest of open science, I will perform an experiment. I will re-publish a series of notebook entries pertaining to one experiment and will write a paper based on that experiment. All of that will be published on the Winnower, since the mechanism is in place to cross-post from this notebook to that site.

The experiment I have in mind is the Repeating Crumley experiment that was the basis for my work on deuterium depleted water. It is the perfect experiment for this trial in ONS publication because the work turned out to reveal a mistake in the original study from the 1960’s, and I also propose a correction to the methods.

The key to this ONS experiment would be to understand what would be required of an open notebook or publication system to be able to provide a complete, organized, and user-friendly documentation system, or at least what is required for proper interaction between an open notebook and a publication platform. Additionally I hope to demonstrate another benefit to open notebook science in an effort to encourage others to participate in ONS.

In the spirit of open notebook science, I will document my interactions here and possibly also on the Winnower, and then write another publication on the Winnower about ONS and the peer-review system.

You can follow the documentation process through my Winnower profile.

Design tips for a killer presentation

I posted this to the Scifund blog but decided to share it with the readers of this site who may not follow Scifund. Enjoy!

Yesterday I provided some motivation for why you should make a great presentation. Now that you are amped up, you should be ready to get to work. But what if you don’t know exactly what to do to separate your presentation from the rest? Well don’t worry, I got you covered. Today I’m going to provide a few simple design tips that you can incorporate into your presentation to give it that wow factor.

The rule of thirds.

If you learn only one thing from this post, remember this rule as it is one of the most basic/important design rules. It is also very handy for photographers and could easily be implemented in your presentation. The setup is easy, just take your artboard (your slideshow page) and divide it into 3 columns and 3 rows of equal spacing (the image here is a 1024×768 px image divided into 9 compartments).

Screen Shot 2013-05-22 at 5.12.53 PM

Now I’ve heard the rule of thirds presented in two ways, and I use both depending on the situation. The primary rule is that the subject of your image should be placed on the grid lines of your slide. If you have intersecting components, for instance a horizon line and a subject, then the intersection of your composition should be placed on an intersection point of your grid. Here is a great example of this in practice:

In this image the hawk is aligned with the right grid line, while the top of the grass (horizon) is aligned with the bottom grid. Using the rule of thirds in this way creates a new level of interest in your presentation, and leaves a lot of desirable white space to enhance the interest in your subject.

The other use of the rule of thirds is to place your entire subject into thirds of the space. This is a bit more difficult for me to explain, so I’ll go right into an example:

Here the flower occupies the entire right third of the image, and the bee occupies the middle third, leaving the final third for white space. In this photo the subject (the bee and the flower) takes up 2/3 of the image space and enhances the interest in the subject. Coincidentally the bee is centered in the image, which might give peace to those symmetry freaks. Bonus points if you noticed that the eye of the bee is aligned with one of the grid intersection points.

One way I use this is presentations is when making an outline (which I really don’t like to do). In the following example, I simplified my dissertation talk into 3 components and used an image to summarize each component:

Screen Shot 2013-05-22 at 5.35.52 PM

There are lots of ways to use this rule in presentations so don’t be afraid to experiment.

Use simple colors for backgrounds.

I’ve seen this violated in business presentations far more times than I have in science, but it still is worth mentioning.

Don’t use backgrounds that have textures, patterns, gradients, or distracting graphics.

It is too distracting to the eye, and your audience won’t be paying attention to you, they’ll be too busy recovering from their seizure. All kidding aside keeping your slide backgrounds simple will make your presentation easy on the eye. Believe it or not, my favorite background is a simple white background with black text. With great contrast comes great responsibility… or something like that.

If you want to go with better eye ergonomics, then use a black background with white text. You get the same level of contrast (maximum!) and you get an added benefit. Think about this from your audience’s perspective. They are sitting in a dark room, getting blasted in the face with bright photons bouncing off the projector. By making the background black the intensity of light reflecting from the screen is diminished and your audience is a little happier. If the lights in the room are at maximum, you may want to stick with the white background so they can actually see the slides.

If you insist on using color, then by all means do so, but stick to solid colors and use a font or image color that provides good contrast to your color. Having a basic understanding of color theory can be very helpful in this regard (See also HSV color space).

Pick quality fonts.

The choice of font will mostly go unnoticed if you go with classic choices like Times New Roman, Calibri, Arial, Myriad, etc. But if you choose to use fonts like Comic Sans (sorry Comic Sans, I had to…) your presentation will definitely be remembered, in a bad way. If you want to go with interesting fonts pick something that fits the theme of your presentation, but make sure it isn’t too distracting. Fonts may make for interesting design, but if your audience struggles to read it at a normal pace they will pay less attention to your message and spend more time trying to figure out what you wrote on screen, why you chose that font, what the funny shapes look like, and then your audience will be lost.

But even picking classic fonts don’t have to be boring. You can pair fonts to make headings enticing and body text readable. For instance, use Times New Roman for titles and Arial for your body. The content will still be readable, but you’ve added a new twist to the presentation. You can even reverse the scheme and go with Arial for the title and Times for the body. Here is a decent beginners guide to pairing fonts. And if you want to find some fun fonts to install on your computer check out some of my favorite resources for royalty free fonts: Da Font, Font Squirrel, and the Lost Type Co-op.

One idea per slide.

All designers advocate for keeping it simple, and some presentation designers incorporate this concept by keeping slides to 3 ideas. I like to take this two steps further by maintaining only one idea per slide. This can be especially handy for presentation styles like Ignite talks. By limiting the slide to just one idea, your audience has no choice but to focus on the one topic at hand and it will certainly make it easier to remember individual points over the remainder of the talk. If you have an image to share, show just the image and remove all the bullets, descriptions, etc (crediting a source is ok though). If you have a list, break the list into its components and put each component on one slide. Make it impactful by just writing the one idea and nothing else. The benefit here is that your audience literally has nothing else to focus on, so after they quickly read the concept they’ll be making great eye contact with you and giving you amazing positive feedback that will energize you through the rest of your talk.

Show only the most relevant information.

This rule is slightly piggy-backing on the previous rule, but comes into play more when you have no choice but to feature more than one object of focus. Presenting data is a good example of this. Most data is complicated, and as the presenter it is your job to simplify it. Making it obvious what your audience should be taking away from a figure is important. Most likely you won’t be on a data set for longer than 3-5 minutes, and if your data is complicated it may take much longer to digest that. Here is an example of some data from my research:

Screen Shot 2013-05-22 at 6.21.17 PM

In this example I was merely trying to show that the higher the concentration of heavy water (D2O), the slower the growth of yeast. As a secondary, I wanted to show the disparity between normal water (DI water, green) and 99.9% D2O (blue). Since it was important that each line be distinguishable, I chose various colors to represent each data set. To help distinguish DI water from 99% D2O, I made those two colors more prominent by making all the other colors more white (in this case I increased the transparency of the other lines). If I simply wanted to distinguish the two lines from each other while showing the other data I could have done something like this:

Screen Shot 2013-05-22 at 6.33.15 PM

In this case I made the extra lines gray so they don’t detract from my message, which is there is vast difference in growth between yeast grown in DI water vs D2O. In this case it’s really easy to distinguish the two data sets I want to feature. But I didn’t want to lose the gradual difference in growth rate, so I simply applied a color gradient to the other sets. As the concentration of heavy water (D2O) increases the color changes slightly.

This is a relatively simple data set to explain, but you can use similar design logic to convey more complicated results. It just takes a little patience to make sure you are really conveying the point you wish to make, and more importantly the information you want your audience to retain.

Break some rules!

Despite all the tips I’ve shared with you, sometimes you can’t convey your message within the constraints of simple design rules. So the final rule is provided, to give you the flexibility you need. But be warned, you should only break the rules if you really need. Here is a slide that is one such example:

Screen Shot 2013-05-22 at 6.41.18 PM

I used a busy background and a list of details to show the differences between hydrogen and deuterium (the stable isotope of hydrogen). I did use the rule of thirds to align the columns, but still I broke lots of rules. But there is a method to my madness.

First, the background was designed to illustrate a point. Each of the little dots is a graphic representation of a water molecule (not to scale). In this case I was trying to show the ratio of hydrogen to deuterium in nature, which is for every 1 deuterium atom there are 6,420 hydrogen atoms in 3,210 molecules of water. So on this slide I placed 3,210 molecules, of which, there is exactly one deuterium atom.

Second, the list was used to highlight the differences between deuterium and hydrogen, which is the one idea of the slide. I don’t expect my audience to remember all these details, I was merely trying to show differences between the two atoms that will later explain differences in the chemical properties of the two water types.

In order to convey my message effectively and impactfully I needed to break a few rules. But I don’t abuse this rule when designing presentations, and you shouldn’t either. Combining the tips provided here will give you the most impactful science talk many of your peers will have personally witnessed. As a final example, here is my dissertation defense in it’s full glory. Take note of my use of each of the rules and try and understand my motivations on slides where I break the rules. If you have any questions feel free to tweet/email me or just leave a comment below.

Advertising in Open Notebooks

I wrote a post a long time ago about potentially funding science through ads in your open notebook (presuming you have one). The conversation was great and included a lot of different perspectives. The one prevailing piece of advice was that of caution. Advertising brings money, when money is involved there is investment, and people tend to feel that their investment warrants voice. When it comes to science there is the potential to be controlled (in whatever capacity that may entail), which is something that should never be incorporated into research.

Interestingly enough, I’m bringing this conversation to light again, but this time it is through practice. If you go to the home page of this site (click the title/banner above) you will see an ad for in the right sidebar, just below my social media information.

I want to make it very clear that the presence of the ad in no way influences my research or post content. The material on this site is free to read and free to use and will always be CC licensed.

I decided to place the ad mostly because it would pay me. Which initially I was against, but after thinking about it I decided to go through with. They didn’t pay me an astronomical sum, but the money I received for the add pays for the website, which allows me to continue to keep the site running for the foreseeable future. This I believe is great for all of you.

Another reason I included an ad, is because I was asked to list the ad. It’s not a google ad that I’m trying to make money from over all time. Right now it is a one year deal and if it doesn’t work out then oh well. Because I was approached about advertising, and someone had spent time analyzing my site, I put some thought into the decision.

I also did it because of the experiment I linked to above. I don’t know if anyone has had advertising on their research site before, but if you can pay for any aspect of your research without government funding then why not? I may get a lot of negative feedback for allowing ads on my site, I may increase the likelihood people have open notebooks knowing they can have self-sufficient, self-hosted websites. I have no idea. We’ll see what happens in the long run regarding this issue.

If you have any comment, concern, or anything to say about me doing this then please, by all means, submit a comment. I also highly encourage you to read the post linked above, which is not my best work but raises some interesting questions. In that discussion, I never thought of specific banner ads, as most of the conversation was directed at Google banner ads, which change depending on the user and site content. With that said…

…share your mind!


@BreakingBio Episode 24: #OpenNotebookScience Edition

I totally forgot to post this when it came out about a week after I defended. The folks who run the hilarious video podcast Breaking Bio had me on as their special guest, with Heidi Smith reporting live on location. Check it out:

The Biophysical Effects of Heavy Water – My Defense Presentation

Defense Outline

Just over a week away now…

  1. Introduction
    1. What is D2O?
    2. The history of D2O
      1. Gilbert Lewis:
        1. purification
        2. biological effects
        3. The hypothesis
      2. Joseph Katz
        1. various experiments
    3. Uses of D2O
      1. NMR, mass spec
      2. The need for a D2O adapted organism
    4. Experiments in DDW
      1. use for space travel
      2. cure for cancer?
  2. The effects on life
    1. Tobacco Seeds
      1. The Crumley experiment and repeating the experiment
      2. Tobacco seed germination rate
      3. tobacco seed growth rate in low deuterium concentration
    2. Arabidopsis
      1. arabidopsis growth rate
      2. arabidopsis morphology
    3. E. coli
      1. growth rates
      2. adaptation and adapted growth
      3. morphology
    4. Yeast
      1. growth rates
      2. adaptation – can’t adapt
      3. morphology
        1. stall during cell division
        2. microtubule stabilization in D2O
  3. Molecular effects
    1. Stabilization of biomacromolecules
      1. DLS experiments
        1. Catalase
        2. Ovalbumin
      2. YPD longevity
    2. Investigation of HD exchange
      1. mechanism and exploitation for protein struture studies
      2. FT-IR analysis
      3. Cavity ring-down analysis
        1. low cost measurement of local atmosphere isotopic composition
    3. Effect on DNA
      1. The pursuit of shotgun DNA mapping
      2. optical tweezers
      3. methods
      4. overstretching data
  4. Future Work
    1. Arabidopsis
      1. adaptation
      2. seed growth in low deuterium
    2. Tobacco growth in low D2O
    3. Yeast morphology in taxol
    4. E coli protein expression in D2O and protein structure analysis
    5. DNA
      1. overstretching in D2O with intercalators

Well there is my idea of how to present my dissertation. I’m not sure if/where I should put my discussion on open notebook science. Also there are a couple things that I could see going elsewhere. I could describe the yeast and e. coli stuff in parallel instead of one after another. Also the HD exchange stuff could easily go right after the yeast, e. coli, or even the tobacco seed stuff. What to do…

Otherwise I think the story is pretty compelling: history of D2O and the unanswered question by Lewis. Investigations into D2O effects and trying to understand low D2O concentration effects, effects on macromolecules, and the understanding of large volume/long-term HD exchange.

Any feedback you may have would be GREATLY appreciated. I’ll send you a figshare t-shirt, or if you are XL, I’ll send you a hoodie (but I only have one).