Lotterhos Lab Protocols
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Welcome
Expectations
Getting Started in the Lab
Editing These Protocols with Quarto
General
Ordering Supplies and Equipment
FedEx Account
General Safety Protocols
Shipping of Hazardous Materials
Purchasing
Receiving Supplies and Equipment
Reimbursement
Creating Barcoded Labels
Managing Chemical Inventory
Clearing Lab Waste
General Equipment
Autoclave (OGL)
Scope Camera MVI Nikon SMZ 1000
Freezers and Freezer Alarm System
Opentrons OT-2 Pipetting Robot
NUMSC - Shared Lab Space
Molecular Equipment
Take3 DNA Quantification
PicoGreen Assay
Magnetic Bead Wash
OMAX Microscope and Camera
TapeStation Library Check
Molecular Protocols for Using the BioRAD qPCR Machine
Pipetting
Pipette Decontamination
Seascape Sample Extractions App Use
Outdated Molecular Protocols
Professional Development
Professional Development Resources
Reducing Cognitive Load
How to Publish a Paper
Writing Checklist
Design
Graduate Courses
Chett’s Cold Brew
Molecular Protocols
Types of Ethanol
Determining Barcodes and Indexes for Illumina Sequencing
DNA Extraction (Omega)
DNA Extraction (Qiagen)
Plate DNA Extraction (Qiagen)
DNA Extraction (Spartina)
Gel Electrophoresis
DNA Drying
Illumina Library Prep
Library Quantification
Qubit dsDNA Quantification
RNA Extraction
Solution Recipes
Changing Gonad Buffer
HCl Baths for Qiagen S-Blocks
Stable Isotope Protocol
qPCR For Oyster Disease Detection - MSX and Dermo
Field and Sampling Protocols
Collecting Samples for DNA
Collecting Samples for RNA
Conductivity Loggers
Field Safety Protocol
Oyster Phenotypic Data Gathering
ImageJ & Mapping Oyster Shells
Lab Kayak Care
pH Loggers
Managing Seatables
Water Sampling
Coding Protocols
Bioinformatics Resources
Transferring Files md5
Accessing and Using Defiance Cluster
General Directory Organization
GitHub Figures
Learning to Code
Setting Alias or PATH variable
Pseudo-Parallelize Your Code on the Cluster
Setting Seeds for Reproducibility
Troubleshooting CellProfiler Installation
Basic Unix Commands
Version Control with GitHub
Editing These Protocols with Quarto
Annotation and GO Enrichment
Linear Mixed Effect Models
Imputing SNP datasets
Explorer
Connecting to the Explorer Cluster
Software and Containers on Discovery for Lotterhos Lab
Open OnDemand
Globus File Transfer
Lotterhos Lab vs. Personal Storage on Explorer; Syncing to Github
Example Scripts and Monitoring
Workflow Parallelization Approaches
Optimizing
Parallelization with Array
Instructions for Discovery for Non-Northeastern Personnel
What are VS Code and PyCharm?
Bioinformagics
install iTerm terminal app for MacOS
Advanced SSH-ing
Installing Anaconda and Anaconda Environments
jupyter Notebooks
How to color code your terminal
Outreach and Teaching
All About Oysters: Outreach Workshop
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Writing Checklist
General
Introduction
Methods
Results
Discussion
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Professional Development
Writing Checklist
Writing Checklist
General
It can be helpful to find papers that you like or are similar, especially in a target journal, and find super clear and model your formatting/language after those papers.
Intro - Where do they state the knowledge gap? How is the intro organized? How soon do they mention the study species? How do they emphasize what is novel about their approach?
Discussion - How do they start the discussion? How do they structure it? What kinds of studies do they compare and contrast to? How repetitive are they of the results? Do they cite figures again?
Introduction
Methods
Results
Be prepared to go through 100 different versions of your figures. It’s not just Katie (pers. comm. MLA).
Discussion
Restate thesis/question at beginning of discussion. Summarize the results without being too repetitive of the technical results, but you don’t have to interpret them yet. It’s OK to repeat things from the intro.
Avoid reciting figures again in the discussion, unless citing a new conceptual/summary figure. There are different philosophies on this, but in E&E most of us were trained to avoid it.
If there are debates or major reviews on the subject, make sure to summarize them again
Start each paragraph with a topic sentence describing the theme of the paragraph. If the first sentence is a repetition of the results, revise it. Try to build from a general theme to the literature and debates around that theme, and then how your results fit into the topic/theme. Compare and contrast your results to similar studies. Is what you find the same or different? why or why not? Try to be specific.
Where do you emphasize what is novel about the approach? Try to emphasize novelty throughout the manuscript.
Avoid restating the results. Is there more than one sentence in this paragraph that is restating the results? If so, try to reduce it. A good way to stop yourself from repeating the results too much is to only allow one sentence per paragraph that restates the results
Try to avoid only citing literature on the study species.
Avoid conjecture. If there is a sentence that does not have a citation, consider removing it.
Is this sentence a broad, sweeping generalization? Make sure to cite large scale reviews or metaanalyses to support it. Citing a few empirical examples is also good, but make sure that the citations align with the statement.
Do you have a section on limitations and/or future directions? If not, consider adding it. The structure can flexible, sometimes having limitations/future in each paragraph or subsection can also work.
Do you have a section on conclusions? If not, consider adding it.
Avoid directives. E.g. “we must do x”, “we need to”, etc.
How to Publish a Paper
Design