# EcoEvoDevo Lab


The [Angelini lab group](http://web.colby.edu/aphanotus/) at [Colby College](https://www.colby.edu/).

- [Current Lab Goals](https://hackmd.io/@EcoEvoDevoLab/summer2023plans)
- [Reading List](https://hackmd.io/@EcoEvoDevoLab/EcoEvoDevoLabReadingList)

## Standard operating procedures (SOPs)

- [General Info for Students in the Lab](https://hackmd.io/@EcoEvoDevoLab/general_lab_info) (including [how to get involved](https://hackmd.io/@EcoEvoDevoLab/general_lab_info#Your-role-in-the-lab) and [lab safety](https://hackmd.io/@EcoEvoDevoLab/general_lab_info#Lab-Safety))

### Field biology

- Field work along rural road sides
- [Field work on Maine islands](https://hackmd.io/@EcoEvoDevoLab/fieldworkislands)
- [Insect Macro Photography](https://hackmd.io/s/r1FcQYF-m)
- [A Guide to Bumble Bee Species of Maine](https://bugsinourbackyard.org/wp-content/uploads/2022/05/Bombus.ID_.220511.letter.pdf)

### Entomology

- [Photographing butterflies in the lab](https://hackmd.io/@EcoEvoDevoLab/photographinglabbutterflies)
- Bumble bee anatomy and measurement protocols for
- [mouthparts](https://bugsinourbackyard.org/wp-content/uploads/2023/06/Bombus.mouthparts.200603.pdf)
- [legs](https://bugsinourbackyard.org/wp-content/uploads/2023/06/Bombus.leg_.measures.pdf)
- [wings (landmarks)](https://bugsinourbackyard.org/wp-content/uploads/2023/06/Bombus-wing-landmarks.200601.pdf)

### Molecular biology

- Autoclave
- [DNA extraction](https://hackmd.io/@EcoEvoDevoLab/dnaextraction) using the Maxwell 16 for large, soft samples
- [DNA extraction](https://hackmd.io/@EcoEvoDevoLab/dnaextractionfrombeetles) using Qiagen DNeasy Kit (e.g. for **beetles**)
- [Extraction of high-molecular weight (HMW) DNA](https://hackmd.io/@EcoEvoDevoLab/dnaextraction_hmw)
- [RNA extraction](https://hackmd.io/@EcoEvoDevoLab/rnaextraction)
- [cDNA synthesis](https://hackmd.io/jSX5BEixQomGsWoaeLkrEw#cDNA-synthesis)
- [PCR](https://hackmd.io/@EcoEvoDevoLab/pcr)
- [Agarose gel electrophoresis](https://hackmd.io/@EcoEvoDevoLab/agarosegels)
- [RNA synthesis](https://hackmd.io/@EcoEvoDevoLab/rnasynth) for RNAi and CRISPR
- [In vitro digestion of DNA with sgRNA/Cas9](https://hackmd.io/@EcoEvoDevoLab/invitroCas9assay)
- Realtime PCR
- [Miscellaneous Molecular Biology Methods](https://hackmd.io/@EcoEvoDevoLab/miscmolbio)

### Developmental biology

- [Rearing flour beetle stocks](https://hackmd.io/@EcoEvoDevoLab/rearingflourbeetles)
- [Rearing *Oncopeltus fasicatus*, milkweed bugs](https://hackmd.io/@EcoEvoDevoLab/rearingmilkweedbugs)
- [Rearing *Jadera* ssp., soapberry bugs](https://hackmd.io/@EcoEvoDevoLab/rearingsoapberrybugs)
- [Rearing *Vanessa cardui*, painted lady butterflies](https://hackmd.io/@EcoEvoDevoLab/rearingvanessacardui)
- [Measuring mass muscle](https://hackmd.io/@EcoEvoDevoLab/musclemass)
- [Microinjection](https://hackmd.io/@EcoEvoDevoLab/microinjection)
- [Photomicrography](https://hackmd.io/@EcoEvoDevoLab/photomicrography)

### Computational biology

- [Intro to R](https://hackmd.io/@aphanotus/Rtutorial)
- [Basic Statistics](https://hackmd.io/@aphanotus/StatsInR)
- Geometric morphometrics
- *[`borealis`](https://github.com/aphanotus/borealis): An R package for reproducible geometric morphometric analysis* - This package has been updated recently and more additions and modifications are planned for the near future. Its vignettes need to be updated to provide a good intro to GMM using the current functions in `borealis` and [`geomorph`](https://github.com/geomorphR/geomorph) (which was also just updated). Right now, you can also look at advice on GMM on the [BI376 lab web pages](https://hackmd.io/@aphanotus/BI376Lab). My hope is to consolidate all this information into the `borealis` vigenettes soon.
- [Linux basics](https://hackmd.io/EU18COvqTJOGEHEOkWmnHQ) - A quick introduction of the bash command line
- [Local BLAST](https://hackmd.io/s/B1TBE7tbX) - How to run BLAST in the command line, using custom local databases.
- [GenBank submission](https://hackmd.io/@aphanotus/GenBankSubmissions) for batch sequences
- [Microbiome Analysis Tutorial](https://hackmd.io/@EcoEvoDevoLab/qiime2tutorial)


## Project workflows

- [BeeSeq](https://hackmd.io/@EcoEvoDevoLab/BeeSeq2021) - Neonic effects on *Bombus impatiens* gene expression and microbiome (2021 Update)
- [Cownose ray feeding ecology](https://hackmd.io/s/Skp1GUtb7) - Using microbiome analysis to determine the prey and microbiota of *Rhinoptera bonasus*
- [*Bombus* landscape microbiome analysis](https://hackmd.io/s/HyXGkNF-7)
- [Qiime2 Classifier Update](https://hackmd.io/HbCbPVr2Qx2N5ECsp2WtKA) - Adding SSU rRNA sequences relevant to bumble bees to the SILVA release 132 NR99 dataset
- [*Oncopeltus* transcriptome analysis](https://github.com/aphanotus/morphDE)

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