Category Archives: Open Notebook Science Info

Impact of Electronic Notebooks on Science

#Scio13 Electronic and Open Notebook Session – Background to ONS

If you are going to ScienceOnline 2013 and are interested in attending the Electronic and Open Lab Notebook Session then there are some things you need to know about open notebooks. Luckily I’ve been writing about open notebook science for a while and have been compiling useful information for the benefit of everyone. Feel free to peruse my articles on the subject and be ready to bring some interesting thoughts to SciO13.

About ONS (the introduction)

The Impacts of ONS

As usual feel free to leave comments below, or bring your comments to ScienceOnline 2013. Or better yet, contribute some thoughts on twitter and make sure you @mention me (@Thescienceofant) and my co-moderator Kristen Briney (@brineydeep4) and tag it #scio13.

Copyright Law and Science

A few weeks ago I wrote a post about how using Creative Commons licensing can protect scientists while allowing use/reuse of scientific data and figures. Initially I wanted to find cases between scientists over copyright infringement or even misuse of the CC licenses. I quickly realized I needed a broad understanding of copyright law and decided to begin with that.

I now have a bunch of notes on the subject but am afraid to share those for fears of copyright infringement, but will happily summarize those notes and share my thoughts on how copyright can impact science and open science more specifically.

The basics of copyright

Copyright law is essentially very simple, and has been made increasingly simple since it was originally expanded upon in the US Constitution. The most recent addendum to this statute came about in the 1976 Copyright Act, which defined rights to copyright holders (exclusive rights), how copyright is achieved, and even what does/does not constitute infringement (fair use).

While the law is simple in principle, copyright infringement is not necessarily black and white. In some instances it is questionable as to what is even copyrightable. In others, the matter of fair use is debatable. Even when there is infringement, it can be tough to prove because there are varying degrees of copying or “borrowing.”

To illustrate the simplicity of copyright law here is an outline of the basic principles:

  1. Copyright is applied immediately from the moment any work is tangibly recorded, both publicly and privately.
  2. To be protected a work needs to be original (not novel) and there needs to be a minimum element of creativity (known as expression).
  3. There are several exclusive rights provided to copyright holders (scroll down to the infringement section) that include copying and distribution.
  4. Copyright infringement is a federal offense!
  5. Even though copyright is applied immediately, in order to file suit for infringement a copyright needs to be registered with the US Copyright Office.

If you want to know more about copyright continue reading on, but if you feel you understand the basics then skip ahead to my analysis of copyright application to science.

Continue reading Copyright Law and Science

Can researchers protect their open data?

One of the biggest arguments I hear against open research is the fear about not being able to protect your intellectual property, aka the fear of being scooped.

Can it happen? Of course, but it happens now and in the past in a mostly closed environment. I don’t believe that open publication of research and data is inviting more data theft.

My answer to the point of data thievery is always, you can’t steal what is being shared. But I’ve come to realize that isn’t always the answer, and especially not the answer to which most scientists are looking. That way of thinking requires a major shift in thinking, which science may not be ready for.

With that said, I think the idea of providing information openly to a broad audience is very appealing, if the fear of scooping wasn’t so predominant. Researchers still want their research to remain theirs, so how can we ensure that what we publish on the web remains ours?

I think the answer lies in the legal system.

In industry, and scientific institutions as well, patents exist to protect intellectual property (IP). If a patent is violated, a legal course of action is pursued and the courts decide the verdict and the punishment (should there be one).

Many people forget that copyright laws exist for those who publish on the web. The only real challenge is monitoring for potential violators of those laws. Sure the broadness of the internet makes it difficult to track use and reuse of information, but at the same time new technologies are developed that make this a little easier. For instance, any link to any of my notebook entries notify me, and I check the source.

But in the event that your research is used/reused in a way that you do not approve, there are courses of action that you can take (of course as of this writing I’m unaware of what those may be). There are also measures you can take to help dictate the use of your research. The most famous of which is the use of Creative Commons Licensing.

The Creative Commons essentially did the legal work for content creators to provide them the platform to allow sharing, use, and reuse of their work. You can either waive your copyright completely and put your IP in the public domain (CC0), or you can maintain your copyright but allow it to be shared and allow for others to make derivatives of your work (CC). Essentially the use of a CC license inhibits unlawful usage of IP, while encouraging proper use/reuse and attribution.

While the system isn’t perfect and there are arguments for and against the use of CC licensing, the truth is that something is better than nothing and CC licensing certainly is something. To prove the point, there have been a few cases of lawsuits over the potential misuse of CC licenses (see here, here, and here). I’ll need to do more research into this, but with the support of the science branch of Creative Commons (formerly Science Commons) scientists will be able to (hopefully) ensure IP protection for research and technological development.

While trademarks and copyrights are nice in practice, there is still a lot of theft on the internet, although I would guess that most of it is unintentional. Simply put most people don’t take the time to make sure that they aren’t violating any usage rules. “If it’s on the internet, I can use it as I see fit.”

The only way to stop IP misuse is over proper legal action (as demonstrated above). While I personally wouldn’t pursue that strategy, I am a proponent of this because there is a need for precedents. If no one ever enforces their copyright (or copyleft in the case of CC), then bad behavior may be reinforced. And if scientists knew they could be sued over breach of CC licensing, then many would be inclined to obey the law and potentially adopt it.

If you can be protected while sharing your research, then why not share it?


I have always declared that was research was in the public domain, but have never officially added the CC0 license. The motivation for this was that I wanted to encourage use and reuse without the need for attribution, and so I can avoid the whole gray area and need for legal recourse should the rights be violated.

Finally this past Sunday, I added the a Creative Commons license to officially allow use and reuse of the IP contained in this notebook. Note however that I did not give it the CC0 license. While I still am allowing the sharing of this research, and the ability to adapt it, I’m trying to encourage the sharing of the research used here. So it is all fair game if you attribute the work, and share your work like I have shared mine.

If there is any question about using the research contained in this notebook, feel free to contact me. It’s that easy.




Open Access Explained!

Let’s end the day on a happy note! I came across this video via Twitter and thought I’d share it with you all. If you are reading my notebook, you are probably in the choir, but this video can still give you good arguments why open access is the future and a necessary change.

Produced by PhD Comics; Animation by Jorge Cham; Narration by Nick Shockey and Jonathan Eisen

I know I’ve used a lot of the arguments presented in this video before, especially the bit about access to medical information. The only downside to open access is the cost of publication, which gets put on scientists. My solution for that is open notebook science. Just like I do every day, you can publish your all your research with some explanation for much cheaper than through journal publishers, and you can still publish the neat and tidy results in a journal of your choice after the fact.

Open Notebook Science – SACNAS Poster

I finished my poster for SACNAS on Friday and it is getting printed today. You can check it out via Slideshare and/or figshare depending on your preference. I’ve made it downloadable via both links, but the figshare one won’t alter the original file so I would download from there. Anyways here it is:

Why the world will care about open notebook science

Back in June I was present at the #scienceatrisk meeting hosted by the Library of Congress. As part of day 1 of the discussions, the attendees were presented with a special manuscript viewing of historical scientific documents. I’ll post the images I took of the documents with some stories soon, but I bring this up because seeing these historical documents got me excited. Excited about the history of science, and excited about the future of it as well.

I was excited because I was getting a chance to touch and see several documents from famous moments in scientific history. In that moment I felt like I was a part of the discoveries made at those moments. I got to read the communications between scientists and relive their discoveries along with them. If only the rest of the world had access to these documents, how excited would the public be over being a part of world changing discoveries.

I showed the pictures to everyone who would stand to talk to me, most of them aren’t scientists or even very scientifically literate, but everyone was deeply interested and excited and impressed.

And then I realized, I’m providing this level of access in real-time. Sure right now the experiments I’m working on aren’t world-changing (yet!), but they are just as exciting.

Not too long after the manuscript viewing I presented on open notebook science, and was reintroduced to the importance of my work. Everyone (from what I could tell) was very interested in the concept of open notebook science. They could read about my experiments, read about my thoughts as I plan the experiment, and read about my conclusions while coming up with their own.

After receiving feedback about ONS and based on my own experience with the historical scientific manuscripts, I realized just how important open notebook science can be for the future of science and for its present.

Currently the only bridge between research and the public are press releases, newspaper articles, and blog posts about specific scientific research. But those outlets only highlight a small percentage of all of the research that goes on around the planet. And allow me to let you in on a little secret… there is a lot being studied around the world and it is ALL very interesting!

Imagine being in a library full of the original notebooks from all the most famous scientists, their collaborators, and even their competitors. Being able to see what they think about, how they think, and how they speak and write will bring you much closer to them as people. You will realize that some are eccentric, some are egotistical, some are clever, some are persistant, but they are all like you. You will also get to live the experience of their work and their discoveries along with them. How is that not exciting?

And this is where open notebook science comes in. Through ONS and the internet, people around the world can have access to all the things I just mentioned. The only difference is the experiments are in real-time and you can interact with the scientists as they work. You may even help them out!

Half of the fun of science is being able to share knowledge with the world. The other half is impacting it via that knowledge. I believe that open notebook science can be the gateway to the whole fun of science.