Notebook

Every dated entry: lab work, analyses, protocols and troubleshooting. Use the box to filter by any word (project, organism, tool…) or click a label on the right.

Date Title Type Project
2026-10-15 Rebuilding the OrthoFinder environment on Pegasus with micromamba Troubleshooting Dark Genes
2026-10-15 SATURN: preparing the human and fly immune datasets for the pLM benchmark Analysis Mnemiopsis Phagocytes
2026-10-15 SATURN: OrthoFinder orthogroups, and how six gene groupings place species together Analysis Mnemiopsis Phagocytes
2026-10-09 SATURN: what the ESMC embeddings are, how macrogenes relate to orthogroups, and a K sweep Analysis Mnemiopsis Phagocytes
2026-10-08 SATURN: ESM-1b vs ESMC-600M, ortholog benchmark and macrogene composition across species Analysis Mnemiopsis Phagocytes
2026-10-06 SATURN 4-species: ESM-1b vs ESMC-600M embeddings for macrogenes Analysis Mnemiopsis Phagocytes
2026-05-07 Pdam 31298: Cell Ranger → GeneExt → CellBender run Analysis Cnidarian Stem Cells
2026-01-15 Obtaining sequences for HCR in Nvec Analysis Cnidarian Stem Cells
2025-04-07 Gfas Symbiont Mapping Test Analysis Dark Genes
2025-04-01 BUSCO on Carnegie Gfas genome Analysis Dark Genes
2025-03-04 Troubleshooting velocyto GTF errors for Mnemi Troubleshooting Mnemiopsis Phagocytes
2024-11-27 Orthofinder between coral species for cell type annotation Analysis Dark Genes
2024-10-30 Pegasus conda environments Analysis  
2024-10-04 Re-running Cell ranger on round 2 Mnemi scRNAseq data Analysis Mnemiopsis Phagocytes
2024-09-10 Geneextend on scRNAseq data Analysis  
2024-07-24 CellRanger on KHW NAR scRNAseq data from 20240724 Analysis Dark Genes
2024-07-24 scRNAseq Velocity analysis Analysis  
2024-04-24 CellRanger on Ehrens scRNAseq data Analysis Cnidarian Stem Cells
2024-03-27 16S Central Document Central doc  
2024-03-27 DNA Methylation Central Document Central doc  
2024-03-27 Genome Annotation Central Document Central doc  
2024-03-27 ITS2 Central Document Central doc  
2024-03-27 Metabolomics Central Document Central doc  
2024-03-27 Single-cell RNAseq Central Document Central doc  
2024-03-27 Testing CellRanger mitochondrial genome integration approaches for scRNAseq data Analysis  
2024-03-27 Transcriptomics Central Document Central doc  
2024-01-31 Gfas_Syms_CellRanger_Analysis Analysis Dark Genes
2024-01-22 20240122 Gfas single cell fresh vs frozen analysis Analysis Dark Genes
2023-12-05 Troubleshooting OrthoFinder Troubleshooting Dark Genes
2023-10-24 Direct RNA sequencing on Oxford Nanopore MinION Protocol Lab work  
2023-09-11 Genome Annotation on Galaxea fasicularis Analysis Dark Genes
2023-09-05 Gfas Dark Genes Single cell preliminary analysis Analysis Dark Genes
2023-08-21 Epidiverse WBGS testing Analysis Porites Thermal Transplant
2023-08-07 KOFamScan for P. astreoides Analysis Porites astreoides Genome
2023-08-04 BisSNP Analysis Analysis Porites Thermal Transplant
2023-03-23 KofamScan Workflow Analysis  
2023-03-21 Galaxea Bleaching Trials Lab work Dark Genes
2023-03-15 EpiDiverse SNP Analysis Analysis Porites Thermal Transplant
2023-01-23 Coral processing for TEM imaging Lab work  
2022-11-29 Galaxea Airbrush, cell count, and RNA extraction test Lab work Dark Genes
2022-11-21 Testing BS-SNPer on WGBS data Analysis Porites Thermal Transplant
2022-11-15 Galaxea fascicularis welcome party to the Cnimmunity lab Lab work  
2022-11-08 Coral Nuclei Isolation Tests Lab work  
2022-10-18 Troubleshooting WGBS Scripts Troubleshooting Porites Thermal Transplant
2022-08-12 PJB ITS2 Re-seq Analysis Analysis Porites July Bleaching
2022-04-27 Old Tag-seq analysis for PJB Analysis Porites July Bleaching
2022-04-25 Porites astreoides genome annotation Analysis Porites astreoides Genome
2022-03-21 20220319 PJB ITS2 re-seq Lab work Porites July Bleaching
2022-03-16 Touchdown PCR for ITS2 Lab work  
2021-11-16 Methylseq trimming test to remove m-bias Analysis Porites Thermal Transplant
2021-11-09 ITS2 KW-AH-ES samples Lab work Porites July Bleaching
2021-11-04 20211104 ITS2 Test set for KW-AH-ES samples Lab work Porites July Bleaching
2021-10-22 HIAST2 alignment with Mansour transcriptome Analysis Porites July Bleaching
2021-10-21 NF-CORE Methylseq Thermal Transplant Analysis Porites Thermal Transplant
2021-10-21 Training AUGUSTUS with BUSCO Analysis Porites astreoides Genome
2021-09-30 BUSCO on Pastreoides reference transcriptomes Analysis Porites astreoides Genome
2021-08-26 20210826 Lipid Extraction Species Test Lab work  
2021-08-19 Past genome MAKER rnd 1 troubleshooting Troubleshooting Porites astreoides Genome
2021-07-14 20210713 Carbohydrate Assay Test Lab work  
2021-07-12 20210712 AH Tag-seq Plate Prep Lab work Symbiont Integration
2021-06-30 20210629 Total Protein Testing Lab work Porites July Bleaching
2021-06-25 20210624 Lipid Assay Trial #2 and #3 Lab work  
2021-06-23 20210622 Lipid Assay Trial #1 Lab work  
2021-06-11 Airbrushing Protocol for Porites July Bleaching Project Lab work Porites July Bleaching
2021-05-26 20210526 WGBS PicoMethyl-seq library re-amplification 2 Lab work Porites Thermal Transplant
2021-05-12 20210512 WGBS PicoMethyl-seq library prep for Thermal Transplant Trial 8 Lab work Porites Thermal Transplant
2021-05-10 20210510 WGBS PicoMethyl-seq library re-amplification Lab work Porites Thermal Transplant
2021-05-06 20210506 WGBS PicoMethyl-seq library prep for Thermal Transplant Trial 7 Lab work Porites Thermal Transplant
2021-05-04 20210504 WGBS PicoMethyl-seq library prep for Thermal Transplant Trial 6 Lab work Porites Thermal Transplant
2021-04-29 20210428 WGBS PicoMethyl-seq library prep for Thermal Transplant Trial 5 Lab work Porites Thermal Transplant
2021-04-27 20210426 WGBS PicoMethyl-seq library prep for Thermal Transplant Trial 4 Lab work Porites Thermal Transplant
2021-04-23 20210422 WGBS PicoMethyl-seq library prep for Thermal Transplant Trial 3 Lab work Porites Thermal Transplant
2021-04-16 Symbiont Integration Metabolomics Processing (20210321 - 20210414) Lab work Symbiont Integration
2021-04-16 Thermal Transplant WGBS PicoMethyl Protocol Lab work Porites Thermal Transplant
2021-04-15 20210415 WGBS PicoMethyl-seq library prep for Thermal Transplant Trial 2 Lab work Porites Thermal Transplant
2021-04-01 20210401 WGBS PicoMethyl-seq library prep for Thermal Transplant Trial 1 Lab work Porites Thermal Transplant
2021-03-25 20210325 Symbiont Integration Metabolomics Extractions BATCH 2 Lab work Symbiont Integration
2021-03-25 20210325 Thermal Transplant ITS2 Lab work Porites Thermal Transplant
2021-03-22 20210321 Symbiont Integration Metabolomics Extractions BATCH 1 Lab work Symbiont Integration
2021-03-10 20210309 Thermal Transplant ITS2 Lab work Porites Thermal Transplant
2021-03-04 20210302 Thermal Transplant ITS2 Lab work Porites Thermal Transplant
2021-02-18 Thermal Transplant ITS2 Test Lab work Porites Thermal Transplant
2021-02-08 DNA Extractions for adult homogenates of Porites Thermal Transplant Batch 8 Lab work Porites Thermal Transplant
2021-01-21 20210121 Nanodrop results on Tag-Seq samples Lab work Porites July Bleaching
2021-01-04 20210104 BUSCO on P. astreoides transcriptome assembly Analysis Porites astreoides Genome
2020-12-21 20201221 BUSCO on P. astreoides transcriptome assembly Analysis Porites astreoides Genome
2020-12-03 20201202 DNA RNA Extractions Porites July Bleaching Experiment Lab work Porites July Bleaching
2020-12-03 20201203 Tag-Seq prep for Porites July Bleaching Experiment Lab work Porites July Bleaching
2020-11-30 20201126 DNA RNA Extractions Porites July Bleaching Experiment Lab work Porites July Bleaching
2020-11-25 20201125 DNA RNA Extractions Porites July Bleaching Experiment Lab work Porites July Bleaching
2020-11-23 20201119 DNA RNA Extractions Porites July Bleaching Experiment Lab work Porites July Bleaching
2020-11-23 20201120 DNA RNA Extractions Porites July Bleaching Experiment Lab work Porites July Bleaching
2020-11-18 20201117 DNA RNA Extractions Porites July Bleaching Experiment Lab work Porites July Bleaching
2020-11-12 20201110 DNA RNA Extractions Porites July Bleaching Experiment Lab work Porites July Bleaching
2020-11-12 20201111 DNA RNA Extractions Porites July Bleaching Experiment Lab work Porites July Bleaching
2020-11-09 20201106 DNA RNA Extractions Porites July Bleaching Experiment and WGBS samples Lab work Porites July Bleaching
2020-10-29 20201029 DNA RNA Extractions Porites July Bleaching Experiment and WGBS samples Lab work Porites July Bleaching
2020-10-27 20201027 DNA RNA Extractions Porites July Bleaching Experiment Lab work Porites July Bleaching
2020-10-26 20201025 DNA RNA Extractions Porites July Bleaching Experiment Lab work Porites July Bleaching
2020-10-23 20201022 DNA RNA Extractions Porites July Bleaching Experiment Lab work Porites July Bleaching
2020-10-20 20201020 Adult P.astreoides and AH test sample Metabolomic Extractions Lab work Porites July Bleaching
2020-10-15 20201015 Adult P.astreoides Metabolomic Extractions Lab work Porites July Bleaching
2020-10-14 20201013 Adult P.astreoides Metabolomic Extractions Lab work Porites July Bleaching
2020-10-12 20201009 Adult P.astreoides Metabolomic Extractions Lab work Porites July Bleaching
2020-10-09 20201008 Adult P.astreoides Metabolomic Extractions Lab work Porites July Bleaching
2020-10-07 20201006 Adult P.astreoides Metabolomic Extractions Lab work Porites July Bleaching
2020-08-27 DNA Extractions for adult homogenates of Porites Thermal Transplant Batch 7 Lab work Porites Thermal Transplant
2020-08-20 DNA RNA Extractions on P. astreoides larvae - BEAD BEATING Batch 5 Lab work Porites Thermal Transplant
2020-08-19 DNA Extractions for adult homogenates of Porites Thermal Transplant Batch 6 Lab work Porites Thermal Transplant
2020-08-19 DNA RNA Extractions on P. astreoides larvae - BEAD BEATING Batch 4 Lab work Porites Thermal Transplant
2020-08-16 DNA Extractions for adult homogenates of Porites Thermal Transplant Batch 5 Lab work Porites Thermal Transplant
2020-08-16 DNA RNA Extractions on P. astreoides larvae - BEAD BEATING Batch 3 Lab work Porites Thermal Transplant
2020-08-13 DNA Extractions for adult homogenates of Porites Thermal Transplant Batch 4 Lab work Porites Thermal Transplant
2020-08-13 DNA RNA Extractions on P. astreoides larvae - BEAD BEATING Batch 2 Lab work Porites Thermal Transplant
2020-08-12 DNA Extractions for adult homogenates of Porites Thermal Transplant Batch 3 Lab work Porites Thermal Transplant
2020-08-12 DNA RNA Extractions on P. astreoides larvae - BEAD BEATING Lab work Porites Thermal Transplant
2020-08-07 DNA Extractions for adult homogenates of Porites Thermal Transplant Batch 2 Lab work Porites Thermal Transplant
2020-08-06 DNA Extractions for adult homogenates of Porites Thermal Transplant Lab work Porites Thermal Transplant
2020-08-06 DNA-RNA extractions Porites Thermal Transplant Larvae BATCH 1 Lab work Porites Thermal Transplant
2020-08-05 DNA-RNA Extractions Porites astreoides homogenates, larvae, and adult fragments Lab work Porites Thermal Transplant
2020-07-31 DNA-RNA-Extraxtion-Thermal-Transplant-Porites-Homogenates Lab work Porites Thermal Transplant
2020-07-30 DNA-RNA-Extractions-Thermal-Transplant-Porites-and-Geoduck Lab work Porites Thermal Transplant
2020-02-03 Metabolomics P astreoides sample prep Lab work  
2020-01-13 DNA RNA Extractions Thermal Transplant ADULT AND LARVAE Trial 4 Lab work Porites Thermal Transplant
2019-12-05 DNA RNA Extractions Thermal Transplant Porites LARVAE Trial 1 Lab work Porites Thermal Transplant
2019-12-05 DNA RNA Extractions Thermal Transplant Porites Trial 3 Lab work Porites Thermal Transplant
2019-12-04 DNA RNA Extractions Thermal Transplant Porites Trial 1 Lab work Porites Thermal Transplant
2019-12-04 DNA RNA Extractions Thermal Transplant Porites Trial 2 Lab work Porites Thermal Transplant
2019-12-04 DNA RNA Extractions Thermal Transplant Porites Trial 2 Lab work Porites Thermal Transplant
2019-11-26 Total Antioxidant Capacity Porites June Patch Adult tissues Lab work Porites Nutrition
2019-10-04 Airbrushing and Homogenizing Porites June Patch Adult Tissues Lab work Porites Nutrition
2019-05-15 Citrate Synthase for A. poculata nutrition experiment Lab work Astrangia Nutrition
2019-05-15 SAM ELISA Kit for A. poculata nutrition experiment Lab work Astrangia Nutrition
2019-05-14 Adult coral Homogenate prep and symbiont separation Lab work  
2019-04-18 Astrangia Nutrition DNA Extractions Lab work Astrangia Nutrition
2019-03-14 Citrate Synthase Troubleshooting Troubleshooting  
2019-03-13 Zymo-DNA-RNA-Extract-P.astreoides-Genome Lab work Porites astreoides Genome
2019-03-03 Zymo Quick-DNA Mini Prep Kit Troubleshooting on Adult P. astreoides Troubleshooting  
2019-02-13 Zymo DNA RNA Extraction Protocol Lab work  
2018-10-05 Total Protein Extraction Protocol Lab work  
2018-08-14 Symbiodinium Density Analysis Protocol Lab work  
2018-02-13 February Goals Planning  
2017-11-09 November Goals Planning  
2017-10-16 Lab Notebook Generation Analysis  
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