# Things to bring up in class tomorrow

• mention updating figshare data from lab 5 to include 308L2012 tag
• make sure data is public
• upload other lab data if you want to be a badass and really contribute to science
• share arduino project notes:
• only some people have mentioned anything in any detail
• only some people have even mentioned what they are going to do for their project
• read each others’ projects and contribute!
• this week keep detailed information about item costs and device build (this will make the instructable entry much easier)
• need a notebook entry about your thoughts on ONS and what you think of the notebook platform you chose
• be brutally honest, if you loved it explain why, if you hated it talk about why
• also need another notebook entry about figshare, again be brutally honest
• finally need notebook entry about class, again be brutally honest, we want to know how to make next year’s class and other class’s better based on your feedback. i want best parts of class and worst parts.

# Presentation: “Open Notebook Science: Research in Real-Time” – Outline

I changed the name of my talk on Tuesday from “Open Notebook Science” to “Open Notebook Science: Research in Real-Time.” I figured most students wouldn’t know or care about open notebook science on it’s own, so I added the extra bit to highlight the one aspect of ons that makes people say “That’s so cool!” when I talk about it. I still have a ton of work to do for this talk, but here I’m going to write up an outline and then tomorrow I’ll throw together some slides.

I’m still debating on how to present. I’m a huge fan of mindmeister for presentations, and it could be high impact on the audience, but I’m worried about internet access and website loading times. I can’t believe that is something I have to worry about nowadays. Regardless, I think I’m going to have to stick with PowerPoint, well I’ll be using LibreOffice which is open sourced software and I think is an extension of OpenOffice.

Anyways here is my outline:

1. Basics of ONS
1. values of ons
1. research in real time
2. instant collaboration
1. project ideas/planning
2. protocols/methods
3. data (raw and formatted)
4. conclusions
4. alternative publishing
2. Tools for ONS
1. host
1. wiki
2. cms
1. wordpress
2. drupal
3. joomla
4. blogging platforms
4. if you can add multiple content formats, it can be a notebook
2. supporting software
2. flickr/picasa/etc
3. figshare
4. disqus/commenting system
5. phone apps
6. anything in the cloud that can be embedded!
3. ONS Community – Physics 308L Junior Lab
1. students allowed to choose notebook system of their choice
1. github wiki
3. custom wordpress site via IheartAnthony
2. rules
1. must notebook everything
1. be clear, detailed, and organized
2. must communicate weekly
2. comment in other notebooks what you like/how to improve notebook or technique
3. allowed to “cheat”
1. students in wednesday lab could read the monday labs and use their notes/software/methods etc
2. allowed to surf internet for better tools, software, etc.

I would like to focus more on the benefits of ONS and the success of the lab than I would on building an open notebook. One of the reasons is because building and maintaining an open notebook is a much longer discussion and I would rather it be a discussion than talking at people. For that reason I may give a workshop this summer for students interested in keeping an open notebook.

The other reason is because my goals for this short talk (15 min or less) is that:

• I want to raise awareness of open notebook science (as many students are unfamiliar with it, even in principle)
• I want to show the benefits of ons over traditional note taking and over traditional publication
• and I want to show how a collaborative community would behave, and this is what the lab simulates.

I think I want to start the talk by projecting a hypothetical future. In this future, peer review  publications are either non-existent as we currently know it, or they are reserved for organizing information scattered across notebooks. I will talk about a future where scientists get information directly from other labs, instead of peer review articles. Research is updated in real-time and scientists have full access to step-by-step protocols, raw data, software and code, thoughts, notes, ideas, and anything that may come up during the scientific process.

That future is beginning now and it’s starting with open notebook science.

How does that sound?

Tomorrow I’ll post what I imagine I’m going to say and my first (and possibly last) draft of the talk that I’ll be giving.

# #juniorlab Lecture 5 #sciencescribe RC circuits

I’m really enjoying taking lecture notes as a sketch note. Steve actually thinks it is better than regular notes and I’m starting to agree. Actually several people have expressed interest in learning how to sketch note for class notes, and have commented that it looks like it is better for absorbing information. My only concern would be is it useful when you have to come back to it later?

Anyways today’s lecture was about RC Circuits and the notes are above. There is a small error:

$f_{c}=RC/2\pi$ should be $f_{c}=2\pi/RC$

# #sciencescribe via Twitter! Lightning: Physics and Protection systems by Marvin E Morris

If you can’t guess what happened by the title then here it is: I sketch noted a seminar that was explained over twitter. That means I wasn’t present for the talk, but there was such a flood of information that I was able to effectively organize a sketch note from the experience. I was quite amazed and I decided to do this just minutes before the talk began!

In the junior lab that I’m teaching, I assigned the students to all sign up for twitter and then go to the Friday Physics colloquium and tweet the seminar. Of course they all groaned, but I get the feeling they liked the talk and appreciated the experience.

The point was to show them first hand how useful collaborative learning can be. Each person will only be able to remember certain aspects of the discussion and will automatically be tuned into whatever their interests are. Through Twitter, their collective knowledge can be assembled and they can all learn from each other.

The experience was quite valuable. They actively engaged in the conversation, with each other, with me, and frequently tweeted the things they were most interested in. If you are interested in learning about lightning you can see the feed for a few days here: Lightning at PandA. (I’ll need to figure out how to save tweets long term somewhere, again any help is appreciated.)

And now without further ado, the sketch note you all came to this post for:

# #sciencescribe Junior Lab Lecture 2: Intro to Labview

Steve gave a lecture to the students of Physics 308-L about Labview basics and showed them how to set up an exponential random number generator. This was the basis for their lab assignment. Here are my sketch notes about the lecture, which I think turned out surprisingly well.

# The ethics of open notebooks

During Junior Lab lecture I was given (graciously) 15 minutes to talk to the students about the ethics of keeping an online open notebook. A lot of the things I discussed kinda go without say, but I said them anyway mostly because I think it is important to stress certain points, especially in the context of the lab. I want to establish that most things that the students probably want to do (copy, paraphrase, google, etc) are completely ok, when done right!

Believe it or not, notebooking is a form of journalism. Your notebook has a duty to present accurate and reproducible data, whether it is just for yourself or you publish it to the whole world (like me!). If you go electronic and open then you have an extra duty to make sure the information is readable so others who may come across it can use it or reproduce the data that you are presenting. Basically you have to uphold the integrity of the information you are presenting and the integrity of yourself as a scientist.

And because you are (most likely) updating daily, this is extra crucial. Typically researchers publish a few times a year and so integrity is important internally day-to-day and then publically those few times. When you are open, integrity is key all the time because someone will find mistakes and holes and that can destroy everything (if you publish in a shady manner).

So how do you maintain a great notebook? Well I like to follow the rules of general blogging to get started:

• Accuracy – let’s be honest, you aren’t going to create everything you need in your research, and that means you are going to borrow ideas, information, etc from others. Computers let us do amazing things like copy and paste. Why paraphrase something you found online when you can get it exactly? When you do this make sure you credit the author (see below). When you do create your own content, then keeping an accurate record of everything is vital. If someone can’t follow your work then it can be hard to prove your results. Why bother with this when you can make your notebook awesome and present yourself as a badass scientist!
• Citations and Attribution – You’ve come across some new information that is really useful to you. On paper you have to cite the source, but in a notebook you can just use a name and a link. It’s so easy you have no excuse not to do it! And make sure you cite everything! You found a neat picture? Give credit to the author (because it’s nice to see your work promoted else where) and add a link to the source material. Found a cool method? Link the notebook, paper, etc. Once you get in the habit, this takes no time at all.
• Details – If you think you should write it down, then you absolutely should. In science you can’t have too much information, but you most certainly can have too little. Many times in the past did I not include information because I thought I would remember and low and behold month’s later I forget and was angry that I didn’t include it at the time. Avoid that issue for yourself and others and take the extra 30 seconds to make note of something that happened. Everyone will be much better off for it, I promise!
• Collaboration is key. If others take the time to comment, then take the time to comment back. Make your notebook a source for discussion. If good ideas come from napkins, then notebooks will be the place of the best ideas. But there are some rules you should follow when it comes to commenting:
• Be specific – say what you did/did not like about an entry, what was hard to understand, what was awesome, what was wrong, what gave you the “a ha!” moment. Saying good job is simply not constructive at all. It may be nice from time to time, but overall those comments add no substance to a notebook.
• Be constructive – if you see an error, fix it! But be polite, nobody likes a troll. If you thought something was informative, then say why. If you have something to add then do that too. Share your experiences, because that will make the notebook even better.
• Discuss! – if you read an entry and you have something to say, then say it no matter how trivial it may seem. Who knows what will happen! And don’t just add fixes or comments. Share ideas. My favorite notebook experiences come from my discussion sessions with my advisor. Not only do I have active engagement in my notebook, but I have a saved transcript so I can come back later to try and remember things.
• Also when it comes to collaboration you should make sure it is clear that you are sharing ideas with whomever else you are working with. Point readers to your cohort’s notebook. Link to their data. Give them attributes. They will do the same for you and the experience will be 1000x better!

One of the things I’ve noticed with my notebook is that the engagement with readers is just not there. With the junior lab course, I’m trying to encourage (and force, haha) the engagement to understand what it will take to engage with my unknown audience. By telling the students that all is fair on the internet as long as you do it ethically, I’m hoping to cultivate the community of the class and passively encourage their interactions with each other. We’ll see what happens.

# Open Notebook Science Mini-Community Project

Steve usually teaches a junior level physics lab each year, and each year he introduces the students to open notebook science. Mostly it is just to get in the habit of taking good notes and to do it electronically. This way he is able to easily keep up with and grade the student’s performance.

Seldomly do the students take advantage of the fact there are prior classes that have online notebooks that they can use for leverage in their experiments, and also they don’t even check in with each other. But in class they freely communicate to each other.

This semester I’m TA for the class and all that is about to change. With this class I’ve realized that this is literally a miniature case study into the dynamics of how open notebook science may work. So not only are the students going to be required to take good notes and understand the principles of good, reliable, effective science, but they are also going to be required to communicate!

I hope that by “forcing” them to communicate (I say that in quotes because they would be allowed to do it anyway, but probably won’t) I will get to witness the power of open notebook science in real time and both behind the scenes (their interactions in lab) and as seen by the public (their online interactions).

I really don’t know what I expect from the experience but I hope to learn how effective ONS can be when the community of scientists who follow a notebook actively participate in the experiments and engage in the notebook. Hopefully the students will even teach me a thing or two about community engagement and ONS!

I’ve made a simple web page that lists all the notebooks so that the students can follow the other notebooks and comment and such. Check them all out here. There is a variety of platforms being used. Some students have elected to use the wiki on GitHub (since they already have to use Github for class), others are using Google Docs, and a few are using self-hosted (by me) WordPress sites.

I’m eager to see what happens and I’ll be posting thoughts and updates on here as things happen.