Category Archives: Uncategorized

Reduce Snakemake runtime by collapsing similar jobs into one multiprocessing job

Snakemake is a pipeline management system written in Python. It enables users to encode tasks as rules that describe how to create output files from input files. These rules are written in a Snakefile (similar to a makefile), and are chained … Continue reading

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The Awsomics bioinformatics framework

Analysis of genomic data has become highly complicated, and a focus of modern biomedical research. Individual labs have growing needs to analyze different types of genomic data in a customized fashion to meet unique research goals. No matter the genomic … Continue reading

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Analysis of high dimensional data: a customized workflow

Genomic data are often high-dimensional. For example, a typical transcroptome data set has less than 100 samples, but over ten thousand genes/variables. This article will introduce a three-part workflow of analyzing high dimensional data: t-SNE for dimension reduction; dbSCAN for sample classificataion, and plotly for visualization. … Continue reading

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Gene function prediction: insights into the correlation of protein and mRNA

How often are we trying to compare the transcripts to the protein expression levels and it just doesn’t work? Can we really use transcriptome level information to predict cellular phenotype, which is mostly governed by proteins? Recent technological advances to … Continue reading

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Turning Scala code into Spark

Note: reposted from http://anthonycros.com/turn-scala-into-spark/ The other day I found myself explaining to a bioinformatician in our team how we could process some data at scale. She is mostly used to processing data in-memory due to the relative small size of the … Continue reading

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Continuous Integration

Automatic code test with Jekins. Outline Overview Create Jenkins Project Configure Jenkins Project Create Webhook on Github CGI Scripts on a Web Server Acknowledgement Overview It is critical to build and test your application at various stages of its development. … Continue reading

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CHOP CBMi Team Working to Create Health Informatics Community in Botswana

CHOP’s Jonathan Crossette and CBMI’s Dr. Tony Luberti played integral roles in organizing the Botswana Health Informatics Pitso 2012, a conference whose primary objective is to define health informatics and its role in the country of Botswana.  Additionally, discussions will … Continue reading

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