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Maintaining your lab notebook may seem like a pain, but it's an important responsibility for several reasons. For one thing, it helps later generations of Marderers to easily find your data. It keeps people from wasting time doing experiments that someone else has already done. Even if your experiment led to a dead end, that information can be very valuable. Another reason is that it can help you stay organized. I find that writing and pasting into my notebook helps me to think through whatever problem I'm working on and sometimes it gives me some really good ideas. One of the most important reasons to keep a great lab notebook is because it makes Eve really happy.

Starting a new lab notebook

LAB NOTEBOOK GUIDELINES

Setting up your new lab notebook: (you can find examples on this page)

  1. Ask the current lab manager to assign you a notebook. If you're a rotation student or just doing a brief stint in the lab, they should give you a partially filled notebook that may have been used by another rotation student or graduate student before you. The next notebook number in the sequence and your FULL name next to it will be recorded legibly in the latest Lab Summary notebook (located on a shelf outside Eve's office).

    1. If there aren't any more notebooks, the current Lab Manager will get some from the lab supply downstairs. Ideally, if you take the last notebook and the Lab Manager isn't aware of it you should tell them so that the next person doesn't have to wait for the new ones to arrive.
  2. Legibly write the new notebook number and your FULL name on your notebook in permanent marker.

  3. Experimentalists should record what experiments you've done or plan to do, paste plots, traces, file names, etc. Theorists should keep track of how simulations are running, where things are saved, what the results look like, plotted results, etc.  

  4. Dedicate a few pages at the beginning of the notebook for a table of contents, project design/motivations/questions, protocols used, etc. (5-6 pages should suffice).

  5. Start your experiment entries immediately after (see below for what you should include in each entry).

  6. Once you finish your current lab notebook, make a summary of the notebook. It should be essentially a table of contents with enough information to allow someone to be able to find the experiment or plot they're looking for.

    1. DO NOT wait until the last minute! It is best to do this as you go so that when your time in the Marder lab comes to a close you aren't frantically trying to write up summaries for all your lab notebooks at once, among a million other things before you leave, and we don't get left with lab notebooks without summary pages.

  7. Paste a copy of the summary in the notebook and in the Lab Summary Notebook where you signed out this notebook. Label your sign-out entry with the page numbers of your summary page(s).

  8. Repeat.

What goes into a notebook?

Experimentalists - Each Entry: (each notebook#_page number will be a unique code for your experiment)

  • Experiment Date

  • Experiment Title/Type

  • Preparation Details

    • Tank #, Temperature, Crab Arrival Date

    • Diagram of the STG - draw out nerves dissected with labels, Vaseline wells with channel numbers

    • Any damage to the preparation (nerves nicked, cells slightly poked, etc.)

    • Other manipulations (decentralization + location of decentralization, etc.)

  • Data File Names, Location (Computer >> Folder >> ###_### (notebook code_page number)

  • Channels (extracellular and intracellular)

  • Description of the experiment (can include the goal of the experiment, procedure (extracellular and/or intracellular recordings from ___ nerves/cells, front-end on maintained, decentralization, temperature ramps, pH changes, pharmacological agents used and the general motivations for using these protocols/manipulations), etc.

  • Quick Outline of the manipulations by file number - change of solution/temp/drug for files #-#, etc.

  • Detailed list of the protocol (manipulations) for each file (input resistance, continuous, stimulation, etc.)

  • For intracellular recordings, include:

    • Relectrode–(before + after, after zeroing the pipette again)

    • Vout–voltage offset, measured right after the pipette is removed from the cell

    • Rinput(quick tests) over the course of the experiment

    • Note significant changes in activity over time (waveform, spike height, etc.)

  • Example Images of the Raw Data (highlights - control, experimental, washout)

  • Data Analysis

 


Theorists - Each Entry: (each notebook#_page number will be a unique code for your experiment)

Generally, use your notebook as a log of what you’re working on.

  • Experiment Date(s)

  • Purpose of the Experiment

  • Modifications made to Code (or save extra copies with appropriate annotations)

  • How bugs were fixed for future reference

  • Printed plots of any "final product"

  • Values of all parameters

  • Clear notes about how you did what you did, and why you wanted to do it in that particular way

***To give you a good idea of what belongs in there, here are some tips from current and past lab members (please contribute everyone).***

Gabrielle (golden standard) 

I put everything in my notebook. It's a log of what I'm working on, what I've talked about with Eve that day (especially if she had ideas or requests for what to do next), and most importantly it's a catalog of my experiments and simulations. I write down any modifications I've made to my code as well as how I fixed any bugs for future reference. Whenever I do an experiment, I write the date at the top of the page and a short blurb about the purpose of the experiment and any notes about how the dissection went that day. Once the prep is on the rig, I write down where I'm saving the data recordings and what I've called them - this is really important if you share a rig or work on multiple rigs. I name my experiment files after the notebook and page # that the experiment starts on. So for example, an axoclamp data file might be called 802_54_xxxx.abf and be saved in a folder labeled "802_54 data" if the experiment starts on page 54 of notebook #802. After the experiment, I'll print traces from the experiment (usually just the highlights - control traces and traces after applying modulator or whatever) and paste them into my notebook. Then if they're interesting, I'll show them to Eve. Nothing puts her in a better mood than seeing traces and colorful plots in a notebook brimming with them...

Alec

Because most of the work I do is digital, I backup all of my code on my Box account provided by Brandeis as well as on an external hard drive and on Chaos. Printouts of any "final product" plots go into my lab notebook as well as the values of all parameters. It is very easy to lose track of what specifically went into a simulation and replication is crucial, so I make sure to include very clear notes about how I did what I did, and why I wanted to do it. I go through a lot of glue sticks. 

 

Example

Lab book summary example

Lab Book # 802

Gabrielle Gutierrez

 

All experiments in this book were done on Cancer borealis.

Data is on BOREALIS computer in C:\Documents and Settings\Gabrielle\My Documents\Marder Lab\802_data.

Modeling data and figures are in C:\Documents and Settings\Gabrielle\My Documents\Marder Lab\2011

 

Page #

Date

Description

Data File Names

Notes

1

8/1/11

Low calcium recipes

-

 

2

8/8/11

PTX vs LoCa, IC current injs

802_2_0000-0012

 

4

8/22/11

Zero/Lo Ca 2+ , IC current injs

802_4_0000-0032

IC and PY intracell

8

8/26/11

Electrode capacitance test

802_8_0000

 

10

9/1/11

Zero/Lowest Ca 2+ , IC current injs

802_10_0000-0039

IC and PY intracell. Spontaneous gastric activity

14

10/31/11

Figures for Eve’s optogen paper

\Marder Lab\Images\optogen

\January\31\network_3cell_figs

 

16

11/1/11

Circuit with feedback from IC

g_range_yy_feedback.mat and g_range_yy_feedback1.mat

Including parameterscapes and some traces

21

11/2/11

Parameterscapes for feedback

\February\2

Weird switch to slow osc. when feedback is added