| Date | Title | Subtitle | Categories | Description |
|---|---|---|---|---|
| September 24, 2026 | ArcGIS, Jupyter Notebook, and Git | A reproducible workflow for ArcGIS spatial analysis using Jupyter Notebook and versioned with Git | workflow, ArcGIS, JupyterNotebook, Git | Here we want to figure out a simple reproducible workflow that allows researchers to work using ArcGIS Pro’s integrated Jupyter Notebook and back up and version their work… |
| September 21, 2026 | Puget Sound’s marine vegetation management background | Understanding the many groups that coordinate management and restoration of kelp and eelgrass habitats in Puget Sound | policy | Kelp and eelgrass meadows are nearshore habitats that provide physical complexity (aka places to lay eggs and hide from predators) in temperate marine waters. They’re also… |
| May 6, 2025 | Master’s Thesis Committee Meeting #3 | Progress check-in on analyses | committee, presentations | |
| December 13, 2024 | Submitted NGS 16SrRNA sequences to NCBI SRA | Backing up raw sequences from mim_c | lab records, code | Watch this 10min video tutorial: How to Submit to SRA, A Beginner’s Guide |
| November 4, 2024 | Backup your work |
using rsync
|
workflow | It’s good practice to have an active work server that you push code to GitHub, and a backup server that you’re not working in for the large files you generate. In case you… |
| November 4, 2024 | Make a secret tunnel |
use .ssh/config file to connect to a remote server
|
code | Open a terminal ( I opened my WSL Ubuntu terminal 🐧) and make a .ssh directory in the home directory, and then open the nano text editor to write a config file in the .ssh… |
| October 8, 2024 | Submitting NGS sequences to NCBI SRA | Backing up raw sequences from Azenta | learning journey, code | So you got an email from Azenta saying your files are ready for download! Exciting! It’s the moment we’ve been waiting for. What next?? |
| 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 | learning journey, code | Azenta will email you to notify you that your project is complete and is being uploaded to your account on the Azenta sFTP server, where it will be available for download… |
| October 7, 2024 | Bioinformatics Pipeline Roadmap | Transcriptomics analysis of RNA-seq data from embryonic development of Montipora capitata rice corals exposed to PVC leachate | code, coral | We’ve extracted totalRNA and shipped it to Azenta for sequencing… so what happens next? How did we go from working with microcentrifuge tubes in the lab to large files on… |
| October 7, 2024 | Summary of previous research on microplastic leachate exposure in marine invertebrate embryonic development | In sea urchin and mussel model organisms | learning journey, coral | @jimenez-guri2023 either exposed adult sea urchins Paracentrotus lividus to excessively high1 levels of PVC leachate or filtered seawater control for 2 weeks, and then… |
| September 30, 2024 | Ontogenetic Development of Montipora capitata | learning journey, coral | Montipora capitata corals are taxonomically classified in the Domain Eukaryota, Kingdom Animalia, Phylum Cnidaria, Class Hexacorallia, Order Scleractinia, Family… | |
| September 9, 2024 | Grants & Fellowships | A running list of grants and fellowships to keep an eye on | stats, coral | Smithsonian fellowships are offered to individuals who design and develop proposals to conduct independent research. |
| September 9, 2024 | Nikon scope pictures annotation & data collection | Annotating images of embryonic development of Montipora capitata rice corals exposed to PVC leachate | protocols, coral | This guide is meant to be a checklist for annotating categories of embryonic development in Montipora capitata using NIS-Elements BR. |
| September 8, 2024 | Timeline & Goals Planning | committee, goals | This is a timeline of goals and progress made toward wrapping up my Master’s Thesis at UW SAFS. | |
| September 6, 2024 | Statistics for embryo scope data | Exploring data from embryonic development of Montipora capitata rice corals exposed to PVC leachate | stats, coral | What information can we get from looking at the Montipora capitata embryos that were exposed to varying levels of PVC leachate (High: 1mg/L, Mid: 0.1mg/L, Low: 0.01mg/L)?… |
| September 3, 2024 | Nikon scope pictures & slide preservation protocol | For capturing embryonic development of Montipora capitata rice corals exposed to PVC leachate | protocols | Watch ’Mounting Your Specimen’ by Dr. Terry Bruce of Clemson University on YouTube |
| August 26, 2024 | 26-Aug-2024 Embryo RNA Extractions | lab records | 8C9F, 9C9F = 89C91 | |
| August 23, 2024 | 23-Aug-2024 Embryo RNA Extractions | lab records | 4L14F, 5CL14F, 6L14HF = 456L14 | |
| August 21, 2024 | 21-Aug-2024 Embryo RNA Extractions | lab records | 1C14F, 2C14F, 3C14HF = 123C14 | |
| August 20, 2024 | 20-Aug-2024 Embryo RNA Extractions | lab records | 1H9F, 2H9F, 3H9F = 123H9 | |
| August 19, 2024 | 19-Aug-2024 Embryo RNA Extractions | lab records | 4H9F, 5H9F, 6H9F = 456H9 | |
| August 16, 2024 | 16-Aug-2024 Embryo RNA Extractions | lab records | 1L4F, 2L4F, 3L4F = 123L4 | |
| August 15, 2024 | 15-Aug-2024 Embryo RNA Extractions | lab records | 4C14F, 5C14F = 45C14 | |
| August 14, 2024 | 14-Aug-2024 Embryo RNA Extractions | lab records | 1C4F, 2C4F, 3C4F = 123C4 | |
| August 13, 2024 | 13-Aug-2024 Embryo RNA Extractions | lab records, coral | 1C9F, 2C9F, 3C9F = 123C9F | |
| August 12, 2024 | 12-Aug-2024 Embryo RNA Extractions | lab records | 6C14F (single sample ~10 embryos) | |
| August 9, 2024 | M. Capitata Embryo DNA/RNA Extractions Protocol | protocols, coral | For inspiration checkout: | |
| July 10, 2024 | HOBO logger calibrations | Two loggers per temperature bath (2 ambient, 2 hot) | protocols, records | On July 10th I calibrated the HOBO logs to a Kessler NIST K750 RTD Thermometer and an apogee instruments underwater quantum flux PAR meter. |
| July 9, 2024 | Bench Incubation | Lab bench records and environmental logs for the development of Montipora capitata embryos exposed to PVC leachate | protocols, records | On July 5th, 6th, and 7th 2024 we conducted an ecotox assay on the development of Montipora capitata coral embryo development under exposure to PVC leachate at nominal… |
| July 9, 2024 | Coral collections & tank acclimation protocol | For spawning of Montipora capitata rice corals | protocols, records | Describe the Montipora capitata coral colony collections under State of Hawai`i Special Activities Permit 2024-35 and tank acclimation prior to spawn night research… |
| July 9, 2024 | Spawn night protocol | For embryonic development of Montipora capitata rice corals | protocols |
This spawn night checklist was used on July 5th, 6th and 7th 2024 at the Hawaiian Institute of Marine Biology (HIMB) on Moku o Loe in Kaneohe Bay, Oahu. The overarching goal… |
| July 9, 2024 | Experiment Log | coral | Kat and Callum collected 10 distinct Montipora capitata colonies of approximately 30cm in diameter from Kaneohe Bay, Hawaii under permit | |
| May 23, 2024 | Extracting & measuring chlorophyll a & c2 concentrations | … from an anemone-hosted symbiotic dinoflagellate using a ThermoFischer Nanodrop 2000c | protocols, anemones | This protocol draws heavily (and almost exclusively!) from the awesome method paper, “Its What’s on the Inside That Counts: An Effective, Efficient, and Streamlined Method… |
| May 3, 2024 | Single stressor leachate exposure summary | A 48 hour exposure to polyvinyl chloride (PVC) leachate and to aged polypropylene (PP) leachate | lab records | This summary serves as a broad overview and notes of the acute (48hour) single stressor polyvinyl chloride (PVC) and polypropylene (PP) leachate exposure to Anthopleura… |
| May 2, 2024 | All about the aggregating anemone | What, where, who studies it, how, and why! | learning journey, anemones | Anthopleura elegantissima are clonal intertidal anemones that can form flexible symbiotic partnerships with different single-celled algae which provide supplemental sugars… |
| April 23, 2024 | Anemone Leachate Heat Experiment Recipe | anemones, protocols | Collect anemones | |
| April 22, 2024 | How to make a custom respirometry chamber | protocols, anemones | I had to make some custom respirometry chambers for my experiment. Here’s the requirements I needed to meet, and how I did it! | |
| April 15, 2024 | Puget Sound Microplastics | learning journey | What are the commonly measured concentrations of microplastics in Puget Sound, Washington? This goal of this objective is to understand the environmentally relevant range of… | |
| March 30, 2024 | Field collection at Constellation Park, Alki, West Seattle | anemones, lab records | On Saturday, March 30th, 2024 Kip and I collected Anthopleura elegantissima from Constellation Park near Alki in West Seattle, Washington under WDFW scientific collection… | |
| March 26, 2024 | Leachate preparation & dilution protocol | Modified from the lab protocol of Dr. Francesco Saliu and Valerio Isa | protocols |
In order to study the effects of microplastic leachate we have to be able to re-create it in a controlled and defined way. For this, I partnered with Dr. Francesco Saliu and…
|
| March 18, 2024 | Field collection at Owens Beach, Point Defiance Park, Tacoma | anemones, lab records |
On Monday, March 18th, 2024 we collected Anthopleura elegantissima from Owen’s Beach at Point Defiance Park in Tacoma, Washington under WDFW scientific collection permit Tanj…
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| February 22, 2024 | Daily Lab Log | Enter at your peril; This one is for me, not you | daily log | Received confirmation that RNA is in line for QAQC |
| February 9, 2024 | Experimental tank setup | protocols, anemones | Hydra 32HD manual | |
| February 5, 2024 | Measuring photosynthesis | Understanding & Operating the Walz Diving-PAM-II | learning journey, anemones | Photosynthesis is magic. Four proteins embedded in a delicate lipid membrane turn light into sugar. It’s energy transformation! The process by which light energy is… |
| February 5, 2024 | Tides & WX Station Data | How to use the rnoaa package | learning journey | “Air temperature and tide data Air temperature and tide level data was obtained from various sources depending on the location. Hourly temperature and tide data for Toke… |
| January 2, 2024 | Anemone Project Planning | anemones | The objective of this study is to examine the combined effects of thermal stress and marine microplastic leachate on photosynthetic efficiency, microbiome community, and… | |
| December 6, 2023 | Pseudoreplication & Control | How to design a manipulation experiment | learning journey | “the use of inferential statistics to test for treatment effects with data from experiments where either treatments are not replicated (though samples may be) or replicates… |
| December 6, 2023 | How I created & maintain my open lab notebook using Quarto, Git & RStudio | code, learning journey | follow happy git for the useR | |
| November 29, 2023 | Phthalates around the World | learning journey | What are the common concentrations (ug/L) of phthalates measured in seawater around the world? This goal of this objective is to understand the environmentally relevant… | |
| November 19, 2023 | Master’s Thesis Committee Meeting #2 | Options for addressing the need for a solvent control | committee | Introduce issue with lack of solvent control in experimental design - 5 mins |
| November 19, 2023 | Master’s Thesis Progress | learning journey, committee | SAFS Masters Thesis Milestones are laid out here | |
| November 14, 2023 | Making PAE treatments and controls | protocols | I used the EPA 506 phthalate esters mix 1, which comes as a 1mL ampule vial with a glass break-off cap. It includes 6 common phthalates each at a concentration of \(500\mu… | |
| November 5, 2023 | Workflow with Git | For all the times I accidentally commit a file that is too big | workflow |
.gitignore cannot filter files by size — it only filters by path patterns, like filenames, extensions, or directory names. It doesn’t support dynamic criteria like file…
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| August 23, 2023 | Dual DNA & RNA Extraction Protocol | protocols | The aim of this protocol is to take coral fragments that have been snap-frozen in liquid nitrogen and extract both DNA for downstream archaea & bacteria microbiome 16S… | |
| August 22, 2023 | The RNA Inhibitors | A tragic saga of continued troubles | lab records | After shipping 20 samples to the University of Texas at Austin GSAF for TagSeq on June 7th 2023, I got a message back from them on June 28th 2023: |
| August 10, 2023 |
Getting Started with QIIME2 and Jupyter Lab
|
Working from a Windows OS and connecting via VPN to a remote server | code, learning journey |
Sometimes it seems the hardest part about developing a new workflow is deciding where to put it! As I start working on analyzing my microbiome data, I need to have a Linux… |
| July 27, 2023 | Target Journals for Submitting Manuscripts | learning journey | Impact Factor 8.9 | |
| June 22, 2023 | Phthalate exposure to coral embryos methods | M. capitata embryo development and EPA 506 pthalate mix 1 acute exposure experimental methods | lab records, protocols | Plasticizers are a suite of chemicals added to plastic consumer products to increase flexibily. The most widely used plasticizers are phthalate acid esters (PAEs). PAE’s are… |
| June 8, 2023 | Choosing 16S Primers for M. capitata microbiome | learning journey | ” Indeed Cruaud et al. (2014) and Fouhy et al. (2016) show that primer choice has a far deeper influence on microbial community than extraction method, although they did… | |
| May 23, 2023 | DNA/RNA Extractions Overview | lab records | Qubit RNA BR Assay Kit The Qubit RNA BR (Broad-Range) Assay Kit, when used with the Qubit Fluorometer, provides an accurate and selective method for the quantitation of RNA… | |
| 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 | I searched the NDBC map for the stations closest to my collection site at Owens Beach, Point Defiance Park in Commencement Bay, Tacoma. | |
| April 25, 2023 | Dual DNA & RNA Extractions for Montipora capitata coral | lab records | These lab extractions follow the Dual DNA & RNA Extraction Protocol with any deviations, exceptions, or notes explained in detail. | |
| February 6, 2023 | Master’s Thesis Committee Meeting #1 | committee | Introduction - 5 mins |
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