DevOps Madness

 LB + amp agar plate is used in bio labs often.  Preparing agar plates is a good skill to have.  Below are the steps or protocol to do it but I also an online protocol as reference.   The LB in powder form should have proportion information there.  The one I have say dissolve 40g of mix in 1 liter of water.  The 40g is a mixture of NaCL 10g, Trypton 10g, Yeast Extract 5g, and Agar 15g.  The plate I use is 100mm x 15mm.  Below is the scale for reference: I have 10 of these 100mm x 15mm plates and each will take 10mL to 15mL of agar.  If I select to do 10mL per plate so we need 10mL x 10 = 100mL of Agar.  If I select to do 15mL per plate then I would need 15mL x 10 = 150mL.  I feel 15mL is better to give me extra margin or error. I can take a 500mL bottle and will it up to 200mL of water + agar powder.  So, 40g/1.0 liter where 1.0 liter equals to 1000mL.  I can do the following algebra: 40g/1000mL = Xg/200mL then X = 8...

 Recently, I joined the Counter Culture Lab in Oakland CA as an intern.  It is a rather interesting maker space for bio hackery.  My mentor has assigned me to the Bio ArtBot project where I can pickup some basic lab skills.  I am working on transforming e-coli bacteria with plasmid gene which expresses color.  The competant cell we are using is call the DH5-alpha  from NEB (New England BioLabs Inc).  The product number is C2988J which costs $73 to buy as of 2022. Here is a sample transformation protocol: Thaw a tube of NEB 5-alpha Competent  E. coli  cells on ice until the last ice crystals disappear. Mix gently and carefully pipette 50 µl of cells into a transformation tube on ice. Add 1-5 µl containing 100 pg-1 µg of plasmid DNA to the cell mixture. Carefully flick the tube 4-5 times to mix cells and DNA.  Do not vortex. Place the mixture on ice for 30 minutes. Do not mix. Heat shock at exactly 42°C for exactly 30 second...

 Qiime2 is a Microbiome bioinformatics platform.  Emm, what does that mean?  Microbiome is the microorganisms in a particular environment.  Bioinformatics is the application of tools of computation and analysis to the capture and interpretation of biological data.  So, what sort of biological data Qiime2 takes in?  Is it DNA data?  If it is just DNA data, why does it has to be microbiome.  Emm. I would like to build it from scratch using dockerfile : docker build \ -t quay.io/qiime2/core: $( QIIME2_RELEASE ) \ -t quay.io/qiime2/core:latest \ --build-arg QIIME2_RELEASE= $( QIIME2_RELEASE ) docker The actual Dockerfile looks like this: FROM continuumio/miniconda3 ARG QIIME2_RELEASE ENV PATH /opt/conda/envs/qiime2-${QIIME2_RELEASE}/bin:$PATH ENV LC_ALL C.UTF-8 ENV LANG C.UTF-8 ENV MPLBACKEND agg ENV HOME /home/qiime2 ENV XDG_CONFIG_HOME /home/qiime2 RUN mkdir /home/qiime2 WORKDIR /home/qiime2 RUN conda update -q -y conda RUN...

 So, I have an CoMA3 X11 app.  It is a genetic analysis pipeline.  I can run its Docker container on MAC OS like so : docker run -it -e DISPLAY=$IP:0 -e XAUTHORITY=/.Xauthority --net=host --ipc=host -v /tmp/.X11-unix:/tmp/.X11-unix -v ~/.Xauthority:/.Xauthority -v $(pwd):/home sebh87/coma3 bash  Actually, I have to change it to this: docker run -it -e DISPLAY= host.docker.internal:0   -e XAUTHORITY=/.Xauthority --net=host --ipc=host -v /tmp/.X11-unix:/tmp/.X11-unix -v ~/.Xauthority:/.Xauthority -v $(pwd):/home sebh87/coma3 bash but before running it I have to do this  xhost + localhost . It is not too bad since I am using .Xauthority's magic cookie for authentication.  The communication between my X11 client and server is over plan text so not so good.  I would like to run this over ssh instead.  So, I edited the original Dockerfile to this: FROM sebh87/coma3:latest RUN apt update && apt install    openssh-server sudo -y RU...

 There are a number of ways to network containerized app running in separate machines.  Docker offers IPVLAND, MACVLAN, Bridges, and Overlay.  For local development or just a few machines, Bridge and VLANs seems just fine.  As the infrastructure gets more complex, then I am face with the prospect of Overlay.  In that case, I am feeling may be reaching for Kubernetes is better than going for Docker. So, how to bring an on-premise K8S into live?  I am anti-expertise so to bring up a huge chunk of infrastrure like this, I would go for reputable providers such as anthos or EKS anywhere .