Category Archives: Open Notebook

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.

The Open IGERT: Review of the Reviews – Grant Declined

Sorry for the weird title, I wanted to describe as much about this post as possible in the title without making it super huge. Long story short, the IGERT Grant that my peers and I submitted in August has been reviewed and the reviews are in.

The Open IGERT has been declined.

I’m not at all surprised. I knew we were a long shot. And I knew that we weren’t focusing on issues that, while not required or mentioned by the NSF, would be things they would want us to focus on. But, I thought we put together a powerful program. Unfortunately the NSF and their army of anonymous peer reviewers thought otherwise.

So in an effort to improve upon the program I am going to share the reviews with you all, and comment on the reviews. The reviews and the review summary can be found in my Google Drive Folder. Feel free to poke around. For reference, here is the original NSF call for proposals. And so you can skip the link, here is the main objectives of the IGERT call:

  • …NSF recognizes the need to educate and support a next generation of researchers able to address fundamental challenges in
    1. core techniques and technologies for advancing big data science and engineering;
    2. analyzing and dealing with challenging computational and data enabled science and engineering (CDS&E) problems, and
    3. researching, providing, and using the cyberinfrastructure that makes cutting-edge CDS&E research possible in any and all disciplines.

On to the reviews:
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Impact of Electronic Notebooks on Science

Amazing and historic artifacts of science

This is sorely due and highly outdated (for internet standards), but I wanted to share this with the world anyway. Back in June I attended the Science at Risk workshop at the Library of Congress. The workshop brought to light the different aspects of how science is achieved via the internet and I was asked to speak on behalf of open notebook science.

On day 1 of the Workshop, we were provided a special manuscript viewing of some of the most historic and treasured scientific documents that is in possession of the Library of Congress. Check it out below, and feel free to ask me questions about the images in the comment section!

#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.

Dissertation Plan

Here is my dissertation and defense plan. My research is composed of three areas:

  1. Shotgun DNA Mapping
  2. D2O Effects
  3. Open notebook science

All of it will be tied together because of ONS and D2O. Let’s get to it!!!


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