• Data Science class – Project Report

    I took BIOL 419: Data Science for Biologists in Winter 2016. My project group used Jake Heare’s data from https://github.com/jheare/OluridaSurvey2014 for final project. We used various classifiers and visualization to analyze the data. This is the link to final project report: https://docs.google.com/document/d/1QBFr_o29CAuwWlZhbJjLeIPDhjnRwGdHzmOfN4d4b6Y/edit?usp=sharing

  • Analyzing fastq files

    Created another iPython notebook ‘BSMAP-v1′ Used program bsmp-2.74 to compare the files with template genome to observe the methylation pattern. -a is query file -d is reference sequence file (In ‘halfshell’ on OWL) -o is output alignment file (Saved in ‘analyses’ folder in ‘Mrunmayee’ (OWL server)) Others used for creating methratio_out_{i}_b.txt files: -u = report »more

  • using IPython and command line

    Trying to open and work with notebook and command line by myself turned out to be more difficult than I thought. All the commands and code I used on Wednesday and Friday: Type ‘cd <drag the directory> ipython’ to select that as a directory in command line To open the notebook ‘ipython notebook’ in command »more

  • Summary of new project

    Comparing the DNA methylation pattern of oysters to see if the location the oysters are planted at changes the expression of some genes. The oysters had parents from the same the location. Half the number of oysters of F1 generation were planted at Fidalgo Bay and the other half were planted at Oyster Bay Things »more

  • DNA Extraction 1/20/16

    The four oyster DNA samples ( 2HL # 28 – 31) incubated at 60 degree for an hour. Samples were previously stored at -80 degrees. DNA was extracted from them using the mollusc DNA extraction kit. None of the optional steps were performed. Later the samples were stored in refrigerator in box ‘Oly gDNA Oly »more

  • DNA Extraction 1/14/16

    The four oyster DNA samples ( 2HL # 24 – 27) incubated at 60 degree for an hour. Samples were previously stored at -80 degrees. DNA was extracted from them using the mollusc DNA extraction kit. None of the optional steps were performed. Later the samples were stored in refrigerator in box ‘Oly gDNA Oly »more

  • DNA Extraction 1/12/16

    The four oyster DNA samples ( 2HL # 20 – 23) incubated at 60 degree for an hour. Samples were previously stored at -80 degrees. DNA was extracted from them using the mollusc DNA extraction kit. None of the optional steps were performed. Later the samples were stored in refrigerator in box ‘Oly gDNA Oly »more

  • DNA Extraction 12/17/2015

    The four oyster DNA samples ( 2HL # 16 – 19) incubated at 60 degree for an hour. Samples were previously stored at -80 degrees. DNA was extracted from them using the mollusc DNA extraction kit. None of the optional steps were performed. Later the samples were stored in refrigerator in box ‘Oly gDNA Oly »more

  • DNA Extractions 12/11/2015

    The four oyster DNA samples ( 2HL # 12 – 15) incubated at 60 degree for an hour. Samples were previously stored at -80 degrees. It didn’t seem like there was any tissue in sample #13. DNA was extracted from them using the mollusc DNA extraction kit. None of the optional steps were performed. Later »more

  • 11/25/2015 – photo documentation Oyster Bay