Category Archives: Open Notebook Science Info

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?

Epilogue

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.

Open Notebook Science as a research outlet

Last week I discussed the perspective of open notebook science (ONS) as a science blog, and the potential it has to be an outlet for high quality scientific outreach. Allowing non-scientist readers access to real-time scientific studies can be a very powerful tool to engage an audience and develop an interest in science directly from the scientist! I’ve taken it upon myself to make this endeavor a responsibility and I hope others join me in the cause.

But there is another perspective of open notebook science that is a bit more obvious, that of a primary source of scientific information. This perspective carries several responsibilities that any potential open notebook scientist should understand when making the leap to ONS.

The biggest complaint against ONS that I get from fellow scientists is the increase in signal-to-noise for scientific information. They are right! To a certain extent. Imagine a world where thousands of the world’s scientists publicly record their step-by-step protocols, raw data, interpreted data, and random thoughts. One would expect an increase in the amount of scientific information especially when measured with the amount of current publications and future publications.

But I’ve never heard a scientist complain about the internet, so why would they complain about this? Search engines help you filter out all that noise. The noise being scientific articles containing information that you don’t care about, isn’t relevant, isn’t complete, or just plain wrong.

Personally I’ve been affected by peer-reviewed publications missing information too many times (and even once is too many times for my taste). And this is where ONS can supersede peer-review. The open notebook can contain all manners of important and highly detailed information. And that should be the responsibility of an open notebook scientist: to add as much detail to a project post as possible.

My dad tells me all the time, “It’s better to have too much than too little,” and this rings absolutely true for scientific information. There have been countless times that I haven’t included every bit of information in a post (back in my OWW days) and then come back to that post wishing I had written the little bit extra that I needed to know.

But there is a little caveat that will lead us to our next responsibility as open notebook scientists: make sure that information is high quality. It can be important to post information that is from failed experiments or results that disprove the current hypothesis, but try to avoid posting flat out wrong/misleading information at all costs.

If open notebook scientists get a reputation to not be trustworthy, the whole movement could collapse before it builds tipping point momentum. It is our responsibility to make sure that the science we publish on a daily, weekly, monthly, etc basis is high quality scientific information. After all we want to be good scientists, and ONS can lead us there faster than the traditional model.

But what if an open notebook scientist publishes a mistake? Well that brings us to our next responsibility: honesty! It’s ok to make a mistake, everyone does. But own the mistake, don’t hide it, don’t cover it up, and don’t lie about it. Open notebook scientists should be advocates of great science, and full transparency will reveal that. Cover ups don’t even survive the traditional process, it just takes longer to reveal bad science. With full transparency mistakes and bad science (intentional/unintentional) will be revealed much faster.

A peer-reviewed retraction is a big deal because of all the time and effort that went into that publication. Your reputation will take a big hit if you have to go through that. With ONS a mistake is less costly, because you have time to acknowledge and correct the error. This ultimately will lead to a higher quality of science.

Open notebook entries are frequently held as more informal writings (compared to peer-reviewed publications), but following the responsibilities outlined here you’ll find yourself treating each entry with the integrity of a short peer-reviewed publication. And that’s the way it should be.

The reputation of your lab and yourself are at stake. But even more so the reputation of the open science community is also on the line and we all want to look good… together!

The impact of electronic and open notebooks on science: session at #SciO13.

It looks like I’ll be co-moderating a sequel to my Scio12 presentation on Open Notebook Science. This year I’ll be joined by Kristin Briney who is a Chemist by training and has become fascinated with electronic notebooks and the technical aspects of such and is now an Informational Librarian (I met so many of those in the past year, they’ve become my favorite people!). She also makes beautiful things!

We’ll be leading a discussion on electronic and open notebooks. We’ll start with the basics of electronic/open notebook platforms and delve into the more philosophical questions I’ve been asking for the past few months. Hopefully we’ll have time to hear about the Physics Lab I taught, which was an experiment in an open notebook community, and about the IGERT grant I co-wrote to train future open notebook scientists (and progress of the grant up to that point). And I’m sure Kristin has been/will be up to some amazing things by then too.

Here is a description of the session:

Publication hasn’t changed much in the last few centuries. In fact the biggest change is publishers switching to an open access model in the last 10 years! As science becomes more electronic, access to that information should be more attainable, but with the current state of publishing that information is locked down. Electronic, online, and open laboratory notebooks could be the key that pushes science to adopt a more open model of publication. By sharing experimental details in real-time the scientific process can be enhanced greatly by allowing access to raw data, detailed methods, and even experiment planning. We discuss the technical and philosophical merits of maintaining electronic/open notebooks. On the technical side we will discuss available tools and current best practices and confront issues of data management and long term archiving. Philosophically we debate the role that open notebooks may play in converting traditional scientists to adopting open access models, and the potential broader impacts they may have on the public perception of science. We hope to leave with better ideas of how to face challenges that electronic/open notebook scientists may face technologically, culturally, and professionally.

Leading up to the conference we’ll be asking a bunch of questions to get the conversation started online. Here are some things we have in mind:

  • How can we convince scientists to make the transition to open/electronic lab notebooks?
  • What are the best platforms for electronic and online lab notebooks?
  • What are the long term implications of keeping an open/electronic notebook?
  • What are the responsibilities of keeping an open notebook?
  • How do scientists deal with terms of service/ownership of research notes when sharing online or storing them in the cloud?
  • How do researchers manage their first electronic notebooks to ensure information retention as lab notebooks evolve?
  • Why are scientists so slow to embrace the open model?
  • Should scientists consider notebooks as a source of outreach?
  • Can open notebooks become an alternative source of publication?
  • Should electronic notebooks be treated the same way as the shared data which they contain?
  • Would a network of open/electronic notebooks provide better access to information, ease issues with storage/archiving, and create a greater sense of (open) community?

Feel free to get the conversation started here in the comments or any other post I write under the Scio13 category (accessible via the sidebar to the right). I hope to see a lot of you at Scio13 and in our session. We have a lot to talk about!

Open Notebook Science as a science blog

I’ve been sharing my research openly as an open notebook for 4 years now, and this past year I’ve been undertaking this endeavor using the WordPress content management system. When I first started with WordPress, I would hear my notebook constantly referred to as my blog. It is true that the layout is of a blog, but I was doing open notebook science, I’m not blogging.

Unfortunately every now and then I would write a post, just like this one, that was not related to the story that my research was telling. I would write posts about open notebooks, open science, or just my random thoughts in general.

I still do.

So of course, me defending my “blog” as an open notebook and maintaining that as a separate entity became more challenging. But maintain I did.

Until I presented in front of esteemed colleagues at the Library of Congress. I began my presentation telling the story of how my notebook wasn’t a blog. Everyone always confuses it with a blog but I argue the differences, until they just concede that they won’t change my mind. It wasn’t until the morning of the presentation that I embraced my open notebook as a blog.

I continued my story in front of a room of the most important people I’ve ever met in my life. I explained how I forgot to email myself a link to the presentation that I created on Mind Meister. And I thought about it for a while and I had nothing with me to send myself the link. Then I realized, that because of my nature of openness I knew exactly where my presentation could be found… on my blog!

Luckily for me, all the build up about how I would never consider my open notebook as a blog paid off and I got a good laugh from the room, and hopefully I got a good one from the most prominent science blogger I know, Bora (@BoraZ).

And from there I continued to explain how my notebook worked and what it means to the world. And ever since that day I’ve thought a lot about this: open notebooks actually have two responsibilities. The first is they create a “paper trail” of scientific information that can improve the efficiency of the scientific process. The second is scientific outreach, and that is attainable through the view of an open notebook as a science blog.

Science bloggers take their work seriously. They understand they have a responsibility to enhance the public’s perception of science. Science blog posts must be accurate and informative, but be accessible and readable, and that is not easy. And the hardest part is that while maintaining scientific integrity, the articles produced must be entertaining and interesting. Putting all that together is not easy and extremely important.

While the main function of science blogs is to make science fun and educational, engaging the audience actual provides an immeasurable service. By informing the public about scientific research and how it impacts their daily lives, bloggers are showing that science isn’t just for nerds. It shows the importance of science and scientists, of which public opinion has dwindled over the past few decades.

Instead of praising scientists for the goals produced by the many varieties of experiments and the diversity of research, people question whether it is all worth it. The government limits spending on research more and more, and the public demand these actions.

But why is this?

I think a lot of it stems from the fact that many people are uninformed as to what research actually is, what it provides, and what scientists actually do. But science blogs and bloggers are improving these perceptions every day. And open notebook science can help!

New Mexico is home to two of the most well known national labs, Los Alamos and Sandia, and two major universities, UNM (where I am) and New Mexico State. There are very few people who actually know about the research that is undertaken at those facilities. The worst part is even at each location it isn’t well known what other research is being conducted.

The saddest part about it is the local community is very interested in understanding what goes on in their backyard, but these facilities provide no outreach unless something groundbreaking happens and the result is a press release.

A network of open research notebooks/blogs would go a long way in bridging this gap between public understanding and actual research. Scientists writing about their own research provides the chance for others to interact directly with the scientist allowing them to ask questions, provide feedback, and maybe even lend a hand. This kind of interaction could lead to very interesting developments, with the scientist perhaps seeing things he wouldn’t have seen before.

Another benefit would be a deeper level of interest in science from the public. More children may be interested in science from a younger age. More students may be encouraged to enter a PhD program. More amateur scientists may emerge. And perhaps funding for research and research training grants (like the IGERT) may emerge.

Just the other day, a friend of mine in Stanford put a status message that said “live-blogging my experiment” so I asked him to send me the link. He showed me his real-time notes and it got me interested in his experiment. I was actually really excited about the level of interaction that I had while another scientist was doing an experiment, and I bet there are a lot of people out there that would be as excited or more so.

What if members of the local community could get live updates on your experiments, watch the experiments unfold, and offer insight into what you’re doing? The benefits of ONS in terms of science outreach could be huge. But more than that, I think open notebook scientists have a responsibility to provide that outreach. I’ve taken it upon myself to carry it out. Will you join me?

 

Dual blogging: The time commitment for keeping an open notebook

One of the top questions I get asked (or comments that I receive) is how much time do I spend on my notebook? It’s sort of a loaded question I think. If I say I spend a lot of time writing in my notebook then my audience, which is already looking for an excuse not to have an open notebook, will be turned away. “I don’t have enough time for that.” On the flip side, if I say it doesn’t require all that much time then the scientific integrity of my research is debated.

It’s human nature to take the easy way out. And as such scientists don’t want to spend countless hours keeping their notebook up to date. This is understandable, but it is foolish to think that keeping a notebook requires very little time to update.

I always forget to respond, but when I’m asked “How much time do I spend keeping up with my notebook?” I should reply, “How much time do you spend maintaining your paper notebook?”

While the two platforms aren’t necessarily the same, the question gets the scientist to think about their own workflow, realizing that they already keep a notebook and if they are a good scientist then it will be full of detailed information, which requires a decent amount of time. The only real difference between an open notebook and a paper one is the word open, technically.

Having an open notebook doesn’t require having a fancy blog, website, social media campaign, etc. All you need is to somehow publish your notes to the internet, and simply put that can just be scanning in your notebook and pushing it to facebook (an account most people already have!). If you are even slightly tech savvy, you can complete this task with minimal time each day (using your phone camera and the facebook app), on the order of 2 minutes! There is literally no excuse to not be open in this scenario.

But what if you want to have a completely electronic notebook that is as detailed as it gets. Let’s take my notebook for example, how long do I spend writing posts and updating information? The most time consuming aspects of my notebook are my introduction posts and my protocol posts.

The introduction posts have to make sense to my audience without having to search for too much background information. In order to accomplish this, I have to spend some time thinking about what I want to say and how to say it simply and this takes time. And the protocols take time because I want my setup to be as detailed as possible so no one needs to struggle to replicate my work.

My results posts usually take the least amount of time because I’m just posting data with some quick thoughts as I still have them. All the analysis is done external to the post so usually my thoughts are ready to transcribe. And posts that are of raw data require the least amount of time because those are just pure information without the need for translation, or analysis. I may write down a quick idea here or there, but most of the time it’s just pure science.

The notebook entries that require the most time are entries like this one. These are the posts that are informational and mostly external to my core research. I need to really think about what I’m going to say and how I’m going to say it, and it ends up being written more as a formal blog post then a typical notebook entry.

The key for managing the open notebook and my research without wasting time or effort is that I’ve completely adjusted to being 100% electronic. I usually have a laptop, tablet, or my phone with me at all times. Notes are transcribed in real-time as the research happens. I write my methods immediately after setting up and experiment (usually that time is dead anyway), data gets published as it is collected and again once it is organized, and results are written at first opportunity. I’ve essentially cut out the middle-man which would be the paper notebook.

If you are interested in keeping an electronic open notebook then I suggest you do the same. Get used to writing electronically. There are a lot of services that can actually help you save time. You don’t need to write a table of contents, you don’t need to paste pictures, you don’t need to remember where you keep information. You may find that you are more efficient because you are paperless, like I have.

 

Dual Blogging: Aspects of Open Notebook Science

The next post on open notebook science is up on Science Exchange, and here is a little snippet for your consumption:

The most important feature of an open notebook is accessibility. Your notebook must be accessible to yourself, and secondly to others. This means that you should be able to access the information whenever and wherever you are, so make sure you have a reliable hosting service. Access to others is equally important, as you have a responsibility to ensure the information is easy to find as well, necessitating an organized notebook with enabled search indexing.

And as a supplement to that I elaborate on the accessibility part of the article in an old notebook entry that you can find here. And for that there is a piece of information that I didn’t get to elaborate on in the Science Exchange post (that I really should write an entire article about somewhere):

Your notebook should be accessible. Not everyone understands what you are talking about, so there is nothing wrong with spending a little extra time to explain the jargony words you decided to use in a post. There are tons of papers that do a poor job of explaining their methods and results in plain english, and open notebook scientists don’t want to fall into that trap. After all, if peers can’t understand your language then your notebook is as useful as not having posted anything in the first place. Ok I’m exaggerating a little in that last part, but accessibility is important. No one wants to spend their time using a translator to understand the jargon in a notebook post.

Tomorrow I hope to have a really useful article up about ONS time management, as the dual blogging continues!

ONS Dual Blogging: Open Notebook Platforms – Supplemental Information and Comments

Up on Science Exchange, I’ve written a post that describes the most ideal open notebook platforms and how they can be used for scientific documentation. Their design is certainly not intended for those purposes, but they are effective tools nonetheless. Here is a sample of the post:

There are consequently an array of open notebook platforms to choose from, and some better suited for certain applications than others. Five such platforms are discussed below, all capable of supporting scientific disciplines in varying aspects.

 

WordPress

 

Originally developed as a blogging platform, WordPress has become much more than that. It is the go to Content Management System (CMS) in web design, and is used for online shopping, blogs, artistic portfolios, personal websites, and even open notebooks. Personally speaking, WordPress is the most versatile platform for open notebooks and should be the model that open notebook designers look toward.

I also go on to discuss Media Wiki, Google Docs, Evernote, and Github. And you can check out the whole post here:

Open Notebook Series: Open Notebook Platforms

I think each service has a lot to offer to open notebook scientists, and with services like Evernote and Google Docs, you could certainly get away with using multiple services. Think combining Google Docs with WordPress/Media Wiki.

The most intriguing service to me is Github. If the wiki was more powerful, Github would be the ultimate notebook in my opinion. The reason is because you can upload any file type to your repository, and there is a social network, and you have access to a wiki to supplement your notebook. I haven’t played too much with the social network component, but if it is even 10% as effective as facebook it could prove very useful.

Github also makes sharing repositories easy and collaboration very easy. Anyone can fork your repository (make a copy to their repository) and if you are collaborating, pushing updates is at the discretion of the original repository’s owner. And it is all versioned in case some files get deleted.

And I’m not sure how true this is, but I’ve heard that Github is open sourced in some capacity so you may even be able to self host your own guthub repository. This would be amazing for ONS and scientists could setup their own lab site to enable collaboration amongst only the members of the lab.

And to further supplement my ONS Platform post, I offer some alternative platforms/tools to aid your open notebooking skills:

Creative Solutions to ONS

There are too many tools on the internet to keep track of, but if you don’t like the options that I mention in my post, here are a few creative alternatives that you may appreciate.

  • Flickr/Picasa – Do you want to keep writing with paper and pen? Try taking pictures of your handwritten notes and upload them to one of the many photo sharing websites. I’ve done this from time to time and upload the image files here to supplement my notebook, when I don’t want to rescribe all the work I’ve already done.
  • Social Media – The real-time capabilities of social media gives you the outlet to post what you want when you want it. Steve and I have used FriendFeed to take notes in real-time before facebook had the feature, and essentially you can do this from any social media platform available. If you use a platform like WordPress/Media Wiki, you can even embed your FriendFeed posts into your notebook and people could see your notes in real time in your native platform.
  • Tablets/SmartPhones – There are plenty of apps that let you take notes, share images/videos, bridge platforms and publish to the web right from your phone/tablet. Who says you need to be tethered to your lab pc?
  • Blogs – I’ve already talked about WordPress, which is more than a blog. But blogging services like Blogger and Tumblr offer comparable features. Blogger is trying to be more like a CMS, but still doesn’t have all the functionality of WordPress, but the Google Suite of Apps helps ease the burden quite a bit. Tumblr however is more limited in its capacity, but if you are going with just text and images for your notebook then it will suit you just fine.
  • Wikispaces – Quick and easy wiki setup in the cloud. No need to self install like Media Wiki, but also not as customizable.

And if you use a tool that I haven’t mentioned I’d love to hear about it and how you make it work for you. ONS doesn’t work if it is tedious and you don’t want to update. The goal of technology is to enhance your workflow and make life a little easier. And I’ve found that the tools and platforms I mention above and in my post at Science Exchange aid my quest for scientific domination.