Category Archives: reproducibility

MMETSP re-assemblies

*** Update (9/27/2016): 719 assemblies now available at the links below. All FINISHED!!! *** Update (9/22/2016): 715 assemblies now available at the links below. I have *almost* finished re-assembling de novo transcriptomes from the Marine Microbial Eukaryotic Transcriptome Sequencing Project (Keeling … Continue reading

Posted in Bioinformatics, cluster, Data Analyses, MMETSP, reproducibility, science | Leave a comment

Computing Workflows for Biologists – Dr. Tracy Teal

I’m so excited to be visiting the Microbial Diversity Course at the Marine Biological Lab in Woods Hole, Massachusetts right now. Really enjoying talking to students and faculty working on projects related to microbial communities, aspects of microbial metabolism, microbial genomics, transcriptomics. … Continue reading

Posted in Data Analyses, reproducibility, science, talks, workshops | Leave a comment

DIB jclub, Better reporting for better research: a checklist for reproducibility

By: Lisa Cohen, Camille Scott, Tamer Mansour, Sherine Awad, C. Titus Brown Cross-posted: http://ivory.idyll.org/blog/2015-jclub-etc-on-reproducibility.html Note: at the Lab for Data Intensive Biology, we’re trying out a new journal club format where we summarize our thoughts on the paper in a … Continue reading

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Reproducibility with AWS – NGS2015

Leigh Sheneman, PhD student at MSU in CS. Evolution and learning with digital organisms, applying to real world organisms in the future! http://angus.readthedocs.org/en/2015/week3/AWS-tips.html Start EC2, medium-sized m3.medium is fine. Log in, update and install stuff. We need the packages for the … Continue reading

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Reproducible Research Using Rmarkdown – NGS2015 Week 3

Tutorial by Marian Schmidt, PhD candidate at the University of Michigan and Software Carpentry instructor. Fun presentation! Have used knitR and Rmarkdown for analysis script files before, but I didn’t even know that github could be accessed through the RStudio interface. … Continue reading

Posted in Genomics Workshop, github, R, reproducibility, workshops | 2 Comments