Posts
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May 6, 2025 | Master’s Thesis Committee Meeting #3 | Progress check-in on analyses | 4 min |
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December 13, 2024 | Submitted NGS 16SrRNA sequences to NCBI SRA | Backing up raw sequences from mim_c | 4 min |
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November 4, 2024 | Backup your work |
using rsync
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3 min |
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November 4, 2024 | Make a secret tunnel |
use .ssh/config file to connect to a remote server
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2 min |
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October 8, 2024 | Submitting NGS sequences to NCBI SRA | Backing up raw sequences from Azenta | 2 min |
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October 8, 2024 | Transfer data files from Azenta to a local server | Getting raw NGS fastq sequence files off Azenta Genewiz server to a local server using Command Line and SFTP | 2 min |
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October 7, 2024 | Bioinformatics Pipeline Roadmap | Transcriptomics analysis of RNA-seq data from embryonic development of Montipora capitata rice corals exposed to PVC leachate | 3 min |
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October 7, 2024 | Summary of previous research on microplastic leachate exposure in marine invertebrate embryonic development | In sea urchin and mussel model organisms | 12 min |
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September 30, 2024 | Ontogenetic Development of Montipora capitata | 1 min | |
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September 9, 2024 | Grants & Fellowships | A running list of grants and fellowships to keep an eye on | 1 min |
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September 9, 2024 | Nikon scope pictures annotation & data collection | Annotating images of embryonic development of Montipora capitata rice corals exposed to PVC leachate | 3 min |
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September 8, 2024 | Timeline & Goals Planning | 1 min | |
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September 6, 2024 | Statistics for embryo scope data | Exploring data from embryonic development of Montipora capitata rice corals exposed to PVC leachate | 17 min |
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September 3, 2024 | Nikon scope pictures & slide preservation protocol | For capturing embryonic development of Montipora capitata rice corals exposed to PVC leachate | 3 min |
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August 26, 2024 | 26-Aug-2024 Embryo RNA Extractions | 5 min | |
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August 23, 2024 | 23-Aug-2024 Embryo RNA Extractions | 6 min | |
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August 21, 2024 | 21-Aug-2024 Embryo RNA Extractions | 6 min | |
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August 20, 2024 | 20-Aug-2024 Embryo RNA Extractions | 5 min | |
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August 19, 2024 | 19-Aug-2024 Embryo RNA Extractions | 5 min | |
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August 16, 2024 | 16-Aug-2024 Embryo RNA Extractions | 5 min | |
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August 15, 2024 | 15-Aug-2024 Embryo RNA Extractions | 5 min | |
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August 14, 2024 | 14-Aug-2024 Embryo RNA Extractions | 5 min | |
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August 13, 2024 | 13-Aug-2024 Embryo RNA Extractions | 6 min | |
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August 12, 2024 | 12-Aug-2024 Embryo RNA Extractions | 4 min | |
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August 9, 2024 | M. Capitata Embryo DNA/RNA Extractions Protocol | 16 min | |
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July 10, 2024 | HOBO logger calibrations | Two loggers per temperature bath (2 ambient, 2 hot) | 12 min |
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July 9, 2024 | Bench Incubation | Lab bench records and environmental logs for the development of Montipora capitata embryos exposed to PVC leachate | 15 min |
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July 9, 2024 | Coral collections & tank acclimation protocol | For spawning of Montipora capitata rice corals | 6 min |
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July 9, 2024 | Spawn night protocol | For embryonic development of Montipora capitata rice corals | 12 min |
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July 9, 2024 | Experiment Log | 1 min | |
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May 23, 2024 | Extracting & measuring chlorophyll a & c2 concentrations | … from an anemone-hosted symbiotic dinoflagellate using a ThermoFischer Nanodrop 2000c | 12 min |
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May 3, 2024 | Single stressor leachate exposure summary | A 48 hour exposure to polyvinyl chloride (PVC) leachate and to aged polypropylene (PP) leachate | 5 min |
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May 2, 2024 | All about the aggregating anemone | What, where, who studies it, how, and why! | 10 min |
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April 23, 2024 | Anemone Leachate Heat Experiment Recipe | 1 min | |
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April 22, 2024 | How to make a custom respirometry chamber | 5 min | |
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April 15, 2024 | Puget Sound Microplastics | 5 min | |
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March 30, 2024 | Field collection at Constellation Park, Alki, West Seattle | 4 min | |
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March 26, 2024 | Leachate preparation & dilution protocol | Modified from the lab protocol of Dr. Francesco Saliu and Valerio Isa | 8 min |
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March 18, 2024 | Field collection at Owens Beach, Point Defiance Park, Tacoma | 7 min | |
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February 22, 2024 | Daily Lab Log | Enter at your peril; This one is for me, not you | 51 min |
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February 9, 2024 | Experimental tank setup | 3 min | |
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February 5, 2024 | Measuring photosynthesis | Understanding & Operating the Walz Diving-PAM-II | 4 min |
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February 5, 2024 | Tides & WX Station Data | How to use the rnoaa package | 6 min |
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January 2, 2024 | Anemone Project Planning | 9 min | |
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December 6, 2023 | Pseudoreplication & Control | How to design a manipulation experiment | 3 min |
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December 6, 2023 | How I created & maintain my open lab notebook using Quarto, Git & RStudio | 1 min | |
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November 29, 2023 | Phthalates around the World | 9 min | |
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November 19, 2023 | Master’s Thesis Committee Meeting #2 | Options for addressing the need for a solvent control | 13 min |
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November 19, 2023 | Master’s Thesis Progress | 5 min | |
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November 14, 2023 | Making PAE treatments and controls | 5 min | |
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November 5, 2023 | Workflow with Git | For all the times I accidentally commit a file that is too big | 6 min |
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August 23, 2023 | Dual DNA & RNA Extraction Protocol | 21 min | |
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August 22, 2023 | The RNA Inhibitors | A tragic saga of continued troubles | 15 min |
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August 10, 2023 |
Getting Started with QIIME2 and Jupyter Lab
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Working from a Windows OS and connecting via VPN to a remote server | 6 min |
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July 27, 2023 | Target Journals for Submitting Manuscripts | 2 min | |
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June 22, 2023 | Phthalate exposure to coral embryos methods | M. capitata embryo development and EPA 506 pthalate mix 1 acute exposure experimental methods | 9 min |
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June 8, 2023 | Choosing 16S Primers for M. capitata microbiome | 2 min | |
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May 23, 2023 | DNA/RNA Extractions Overview | 4 min | |
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Invalid Date | Environmental Landscape of an Intertidal Heat Wave | Using NOAA National Data Buoy Center (NDBC) to map air and water temperatures in Commencement Bay, Tacoma, WA, during the June 2021 Puget Sound heat wave | 3 min |
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April 25, 2023 | Dual DNA & RNA Extractions for Montipora capitata coral | 25 min | |
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February 6, 2023 | Master’s Thesis Committee Meeting #1 | 20 min |
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