Note: this is a search engine friendly version of my lab notebook, please see the pdf version of this document for a more human friendly, printer friendly version.

Open Notebook Science License

This work is licensed under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 License.

For more information about Open Notebook Science see the following blog articles:

Jean-Claude Bradley coined the term Open Notebook Science
Bill Hooker at 3 quarks daily has a nice series of articles about open science

About the author: I'm J. I'm a graduate student in Tim Gardner's lab at Boston University. For more about me see J's Page.

Notes on organization, comprehension, and raw data availability
Organization: This lab notebook is organized into chapters, which roughly correspond to the different experimental projects I am working on or have worked on in the past.

Comprehension: Prior to making this an open notebook, it was only important that myself and a few other people understand the contents of the notebook (when I want to rest of the scientific world to understand, I polish and organize the stuff into a paper). Since going open, I developed a system of minimal rules to follow so that other researchers have a better chance of understanding the big-picture of each chapter. The newer chapters abide by these rules, most of the older chapters don't yet. I'll try to update them as I go along, or at least I'll reference the paper where the work was published.

Nonetheless, the work in this document will never be as easy to understand or as flowing as a publication in a scientific journal, particularly because it has almost all of the failed experiments that happen along the way to finishing a project. You also may find many speling errors, not good grammar, and a few bad words when experiments are being a pain-in-my-ass.

Raw data availability: I switched to a latex/electronic lab notebook in September 2005. Along the way, I learned different tricks to make this thing more useful to myself. It wasn't until a year or more later that I developed a good system to link to my raw data. If you want any of the raw data that doesn't have a hyperlink to it, send me an email, I can probably dig it up from my computer.

Notes on referencing this work If for some reason you need to refer to this document in your own work do not refer to the page number or the section number, because they change as I add things to the notebook. I try not to change the chapter and section headings, so it's best if you refer to those. Please also include a link to the page where I keep this open science notebook.

Notes on my referencing of other work There are very few references in this document. I do give credit to the appropiate folks when chapters from this notebook are published. Since the notebook is open, I'll try to add key references as I start new chapters in the future.

Notes on completeness I do not release the chapters (currently only one) that involve work in collaboration with other labs, who may not want their research posted on the web prior to more traditional routes of publication. I also do a large amount of bioinformatics stuff and coding. In general, I don't include software in my lab notebook (for this I maintain a cvs and a wiki for tracking stuff). I currently have no plans to post my software as part of this notebook, because much of it is open source and/or published already.

Notes on authorship

The large majority of the work in this notebook was done by me (Jeremiah Faith). However, I have also included "highlights" from some of the very productive rotation students that have worked with me. Details will be found in their own lab notebooks, but I'll put the main conclusions and figures in this notebook, in case they disappear to other labs after their rotations and so that it is clear where some of the conclusions and steps in this notebook derive from. To make clear work that was done by someone else I'll surround each section by any author (besides myself with) like this:

BEGIN WORK BY FIRST_NAME LAST_NAME
Date

work goes here
END WORK BY FIRST_NAME LAST_NAME

Because of the latex formatting engine some of the figures may fall outside that section, but I try reference the authors name in the figure legend.

Names of addition authors Currently the contributors of data for this manual (besides myself) are Kevin Litcofsky and Esther Rheinbay.