Lotterhos Lab Protocols
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Welcome
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Outdated Molecular Protocols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
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
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
Discovery
Connecting to the Discovery Cluster
Software and Containers on Discovery for Lotterhos Lab
Open OnDemand
Globus File Transfer
Lotterhos Lab vs. Personal Storage on Discovery and GitHub
Example Scripts
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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Example Scripts
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Lotterhos Lab vs. Personal Storage on Discovery and GitHub
Workflow Parallelization Approaches