Category Archives: Open Notebook Science Info

Chapter 1: Open Notebook Science

View in Google Drive.

The link above should give you access to the chapter in all it’s glory. Currently it is pretty much done barring revisions, the addition of figures, and moving the references from side comments to an end of chapter reference section. I’m providing an embed below in case you don’t care about all the cool references enclosed and just want to read. If you are reading via mobile, click the link.

The entire story of my scientific career

This article is actually the introduction to my dissertation and I thought I’d share it with the world officially rather than let it die in an electronic archive somewhere. I’ve shared this story in some form or another several times already, but I’ve never provided the entire account like this. And so, it is with great pleasure that I share with you, the story of how I became the scientist that I am today…

I joined the KochLab in the Spring of 2007. It was a brand new lab that, at the time, was comprised of Dr. Koch, myself, and my best friend Larry Herskowitz (who is now Dr. Herskowitz). In our first lab meeting, Dr. Koch discussed his scientific endeavors up to that point (some of which are continued in this dissertation) and introduced the concept of open science.

Open science was, and still is, an emerging paradigm, and is not to be confused with a particular field of science. The core concept of open science is providing access information and it is through the opening of scientific research that many new endeavors have become possible. Many of these endeavors have changed the way scientists approach research and acquire data. Citizen science, for instance, has brought a mass scale of human analysis to previously unsolvable problems. Even sharing data has led to new forms of collaboration. Data repositories have allowed scientists to share data with the world in hopes of finding new uses for the shared data. Tools like DataOne have emerged to provide some organization to the new data. Meanwhile, open notebook science has emerged to open the entire scientific process and practitioners make every stage of research accessible including protocols, raw data, data analysis, and much more open to scrutiny.
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The value of open research

This post is written to supplement the P2PU Open Science Education Module, and in particular is meant to be an introduction to open research education.

My name is Anthony Salvagno and I’m an open notebook scientist. That basically means that I publish ALL of my research in real-time on the web. All of that research is attributed under a Creative Commons Attribution ShareAlike (CC BY-SA) license, so the information is free for anyone to use.

If the foundation of science is the pursuit of knowledge and to share that knowledge, then why is it acceptable for scientists to hide their research? Why is it ok for publishers to make you pay for that information? Why is it scientific culture to protect data like it is a commodity to be sold?

In truth, that system worked in the past because the technology was limited. Now the technology exists to instill a new culture. But what are the driving forces that would push someone to make this change? Simply put, I was fed up!

I was originally pushed into open science for one simple reason: my advisor was trained in an extremely closed system. In my first year of graduate school (and his lab), I was presented with the concept of open science, which then was barely taking hold. I was surprised to learn that scientific culture wasn’t a naturally open system, and in fact was surprisingly opposed to that concept.

Early in my graduate program, I became frustrated with the way scientific publications were written. I could only understand a small percentage of the articles I was reading, articles that were written by my peers. I knew most graduate students felt the same way. If we are producing the data and writing the papers, then why would we continue to perpetuate the cycle? So I decided that all of my research would be as accessible as possible.

At times, I would need to understand an experimental process, so I would scan the literature and try to repeat experiments to gain a foothold. I became frustrated with the content contained in the methods sections of scholarly work. Often, the methods would be vague, condensed, or just incomplete, and it would cost me time and money trying and failing to repeat experiments. So I began to document my protocols completely, including minor details that could potentially save other scientists a lot of time.

I have also come across scientific results of a questionable nature. Most of the time the results seemed incongruent with my own research, or even just based on my own expertise I knew there was no way to achieve those results. But the scientific process lacked transparency, so there was no way to understand how the researchers obtained their data. So I made sure that my analysis was entirely transparent, and I provide the data during every phase of analysis including the raw data.

In essence, I have become the scientist that I am because of the experiences that I’ve had. Instead of perpetuating the problems that exist in modern scholarly work, I work toward making a change.

I know I’m not the only scientist who has come across the same issues, in addition to other ones. There are a lot of open scientists who work toward the same goals. We hope to bring about a new culture to enhance the speed of science, to improve our collective knowledge, and to make discoveries that would be impossible in the old system. That is why open research practices are important to me, and that is why every scientist should be an open scientist.

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.

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