Previous Does[0]Compute Meetings

May 27, 2020 Validating files at each step in a sequence processing pipeline using sequence_handling as an example
Lead by: Chaochih Liu
May 13, 2020 Code/methods does not always equal reproducibility
Lead by: Group Discussion
Apr 29, 2020 Indexing
Lead by: Peter Morrell
Apr 8, 2020 Plink
Lead by: Group Discussion
Mar 25, 2020 VCF Concordance
Lead by: Group Discussion
Feb 19, 2020 GATK's Variant Quality Score Recalibration (VQSR) and exploring VCF files with scikit-allel to identify VCF filtering criteria
Lead by: Group Discussion
Dec 20, 2019 Winter Break. Happy holidays!
Lead by: No one
Dec 6, 2019 Enhancing reproducibility in scientific computing: Metrics and registry for Singularity containers
Lead by: Group Discussion
Nov 22, 2019 Recommendations for performance optimizations when using GATK3.8 and GATK4
Lead by: Group Discussion
Nov 15, 2019 Bioinformatics core competencies to improve bioinformatics training
Lead by: Group Discussion
Aug 30, 2019 Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks
Lead by: Group Discussion
Aug 16, 2019 Nanopore data processing
Lead by: Group Discussion
Aug 2, 2019 READMEs and Reproducibility
Lead by: Group Discussion
Jun 28, 2019 Reproducible Bioconductor workflows using browser-based interactive notebooks and containers
Lead by: Group Discussion
Jun 14, 2019 Samtools WGS/WES Mapping to Variant Calls - Special time: 10:00 AM
Lead by: Group Discussion
May 31, 2019 Performant Python Ch. 10: Clusters and Job Queues
Lead by: Group Discussion
May 17, 2019 GATK 4.1.0.0
Lead by: Group Discussion
Apr 26, 2019 Fast PCA with scikit-allel
Lead by: Group Discussion
Apr 12, 2019 How to use Jupyter Notebooks for Bash and Python programming
Lead by: Group Discussion
Mar 29, 2019 Organized project structure
Lead by: Group Discussion
Mar 15, 2019 Basic data structures in Python
Lead by: Group Discussion
Mar 1, 2019 Unit testing in Python
Lead by: Group Discussion
Feb 15, 2019 Bioconda - Special time 2-3 PM
Lead by: Group Discussion
Feb 1, 2019 Software Publishing Best Practices
Lead by: Group Discussion
Dec 14, 2018 Continued - Manipulating VCF files with scikit-allel
Lead by: Group Discussion
Nov 30, 2018 Manipulating VCF files with scikit-allel
Lead by: Group Discussion
Nov 16, 2018 Archiving publication data with DRUM archives
Lead by: University of Minnesota Libraries
Nov 2, 2018 Introduction to Cloud Computing
Lead by: Group Discussion
Oct 19, 2018 NIH-HCP tutorial: Creating and running software containers with Singularity
Lead by: Group Discussion
Oct 5, 2018 1) Shah N, Nute MG, Warnow T, Pop M. 2018. Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows. Bioinformatics.
2) Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403–410.

Lead by: Group Discussion
Sep 21, 2018 Jupyter Notebook
Lead by: Group Discussion
Sep 7, 2018 Talk by Dr. Wen Wang on: Discovering genetic interactions bridging pathways in genome-wide association studies.
Lead by: Invited Speaker
Aug 17, 2018 fwdpy11: A Python package for forward simulations
Lead by: Kevin Thornton
Aug 3, 2018 Writing Empirical Articles: Transparency, Reproducibility, Clarity, and Memorability
Lead by: Group Discussion
Jul 25, 2018 SLiM 2: Flexible, interactive forward genetic simulations
Lead by: Group Discussion
Jul 6, 2018 A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3
Lead by: Group Discussion
Jun 22, 2018 Nanopore sequencing data analysis: state of the art, applications and challenges
Lead by: Group Discussion - 3:00 PM
Jun 7, 2018 Bioinformatics Algorithms - Ch 9 How do we locate disease-causing mutations?
Lead by: Pair Programming
May 31, 2018 Bioinformatics Algorithms - Ch 5 How do we compare biological sequences?
Lead by: Pair Programming
May 24, 2018 Bioinformatics Algorithms - Ch 3 How do we assemble genomes? - Pages 134-164
Lead by: Pair Programming
May 17, 2018 Bioinformatics Algorithms - Ch 3 How do we assemble genomes?
Lead by: Pair Programming
May 3, 2018 A quick guid to organizing computational biology projects
Lead by: Group Discussion
May 3, 2018 Reproducible workflows
Lead by: Group Discussion
Apr 19, 2018 Ten quick tips for teaching programming
Lead by: Group Discussion
Apr 5, 2018 Broman KW & Woo KH (2017) Data organization in spreadsheets. The American Statistician; doi: 10.1080/00031305.2017.1375989
Lead by: Group Discussion
Mar 22, 2018 Li H (2018) Minimap2: pairwise alignment for nucleotide sequences. Prepring; arXiv:1708.01492v5 [q-bio.GN]
Lead by: Group Discussion
Mar 15, 2018 Spring Break - no discussion this week
Lead by: To be determined
Mar 1, 2018 Wilson Sayres MA, Hauser C, Sierk M, Robic S et al. (2017) Bioinformatics Core Competencies for Undergraduate Life Sciences Education. bioRxiv 170993; doi: https://doi.org/10.1101/170993
Lead by: Group Discussion
Feb 15, 2018 Blischak JD, Davenport ER, Wilson G (2016) A quick introduction to version control with Git and GitHub. PLoS Comput Biol 12(1): e1004668.
Lead by: Group Discussion
Feb 1, 2018 Special Topic: Carey & Papin 2018. Ten simple rules for biologists learning to program
Lead by: Chaochih Liu and Li Lei
Jan 25, 2018 Fluent Python Chapter 8: Object References, Mutability, and Recycling
Lead by: Corey Carter
Jan 3, 2018 Holidays - no discussion this week
Lead by:
Dec 27, 2017 Holidays - no discussion this week
Lead by:
Dec 20, 2017 Holidays - no discussion this week
Lead by:
Dec 13, 2017 Bioinformatics Data Skills Chapter 8: A Rapid Introduction to the R Language
Lead by: Chaochih Liu
Dec 6, 2017 sequence_handling
Lead by: Skylar Wyant
Nov 29, 2017 Bioinformatics Data Skills Chapter 7: Unix Data Tools
Lead by: Erica Sun
Nov 22, 2017 Fluent Python Chapter 7: Function Decorators and Closures
Lead by: Ya Yang
Nov 15, 2017 Bioinformatics Data Skills Chapter 6: Bioinformatics Data
Lead by: Chaochih Liu
Nov 8, 2017 Fluent Python Chapter 5: First-Class Functions and Chapter 6: Design Patterns with First-Class Functions
Lead by: Rebekah Mohn
Nov 1, 2017 Reproducible Research and Best Practices
Lead by: Penny Kianian
Oct 25, 2017 Fluent Python Chapter 4: Text versus Bytes
Lead by: Chaochih Liu
Oct 18, 2017 Bioinformatics Data Skills Chapter 4: Working with Remote Machines and Chapter 5: Git for Scientists
Lead by: Corey Carter and Erica Sun
Oct 11, 2017 Fluent Python Chapter 3: Dictionaries and Sets
Lead by: Corey Carter and Li Lei
Oct 4, 2017 Bioinformatics Data Skills Chapter 3: Remedial Unix Shell
Lead by: Xin Li
Sep 27, 2017 Fluent Python Chapter 1: The Python Data Model and Chapter 2: An Array of Sequences
Lead by: Peter Morrell
Sep 20, 2017 Bioinformatics Data Skills Chapter 1: How to Learn Bioinformatics
Lead by: Chaochih Liu and Li Lei
Aug 22, 2017 fwdpp/fwdpy/fwdpy11 project
Lead by: TBD
Aug 8, 2017 fwdpp/fwdpy/fwdpy11 project
Lead by: TBD
Jul 25, 2017 fwdpp/fwdpy/fwdpy11 project
Lead by: TBD
Jun 27, 2017 fwdpp/fwdpy/fwdpy11 simulation
Lead by: TBD
Jun 13, 2017 fwdpp/fwdpy/fwdpy11 simulation
Lead by: TBD
May 30, 2017 fwdpp/fwdpy/fwdpy11 simulation
Lead by: Colin Pierce
May 16, 2017 fwdpp/fwdpy/fwdpy11 various frameworks
Lead by: Group Discussion
May 9, 2017 Quantitative Genetics Part IV: BEAGLE and fastPHASE
Lead by: Peter Morrell
May 2, 2017 10x genomics data analysis
Lead by: John R Garbe from UMGC
Apr 25, 2017 Population Genetics Part II: ANGSD and ANGSD-wrapper continued
Lead by: Chaochih Liu
Apr 18, 2017 Population Genetics Part I: ANGSD and ANGSD-wrapper
Lead by: Chaochih Liu
Apr 11, 2017 Break, we will resume weekly discussions next week on April 18th.
Lead by: N/A
Apr 4, 2017 Break, we will resume weekly discussions next week on April 11th.
Lead by: N/A
Mar 28, 2017 Big Data Visualization
Lead by: Alex Olhoff
Mar 21, 2017 Quantitative Genetics III: R NAM
Lead by: Alex Olhoff
Mar 14, 2017 Quantitative Genetics Part II: R/QTL continued
Lead by: Tom Kono
Mar 7, 2017 Quantitative Genetics Part I: R/QTL
Lead by: Li Lei
Feb 28, 2017 Variant Annotation Part: BAD_Mutations and ANNOVAR
Lead by: Tom Kono
Feb 21, 2017 Variant Detection Part III: VCFtools and Platypus
Lead by: Paul Hoffman
Feb 14, 2017 Variant Detection Part II: SAMTools mpileup and Freebayes
Lead by: Peter Morrell
Feb 7, 2017 Variant Detection Part I: Genome Analysis Toolkit
Lead by: Li Lei
Jan 24, 2017 sequence_handling
Lead by: Fernanda Rodriguez
Dec 15, 2016 Genomic Ranges
Lead by: Chaochih Liu
Dec 1, 2016 Advanced Software Installation
Lead by: Paul Hoffman
Nov 17, 2016 SAM Processing II
Lead by: Colin Pierce
Nov 10, 2016 SAM Processing I
Lead by: Li Lei
Nov 3, 2016 Long Read Aligners
Lead by: Kevin Silverstein and Corey Carter
Oct 20, 2016 Short Read Aligners II
Lead by: Ying Zhang
Oct 20, 2016 Short Read Aligners I
Lead by: Peter Morrell
Oct 6, 2016 Sequence Cleaning and Quality Control II
Lead by: Chaochih Liu
Oct 6, 2016 Sequence Cleaning and Quality Control I
Lead by: Paul Hoffman
Sep 29, 2016 File Conversions and Other Utilities II
Lead by: Chaochih Liu
Sep 22, 2016 File Conversions and Other Utilities I
Lead by: Li Lei and Paul Hoffman
Sep 9, 2016 Data Science from Scratch Chapter 12: k-Nearest Neighbors
Lead by: Li Lei
Aug 19, 2016 Data Science from Scratch Chapter 11: Machine Learning
Lead by: Kevin Silverstein
Aug 5, 2016 Data Science from Scratch Chapters 5-7: Introduction to Statistics
Lead by: Chaochih Liu and Skylar Wyant
Jul 22, 2016 Data Science from Scratch Chapter 1: Introduction and Chapter 4: Linear Algebra
Lead by: Connor Depies and Felipe Reyes
Jul 8, 2016 Becoming a Better Programmer Chapter 3: Write Less Code!
Lead by: Chaochih Liu and Peter Morrell
Jun 24, 2016 Data Science from Scratch Chapter 9: Getting Data
Lead by: Skylar Wyant and Felipe Reyes
Jun 10, 2016 Types and Typing Systems: Chapter 3 from Cython
Lead by: Paul Hoffman
May 20, 2016 Chapter 8: Modules and Testing
Lead by: Skylar Wyant and Colin Pierce
May 6, 2016 Chapter 7: Exception Handling
Lead by: Li Lei and Peter Morrell
Apr 22, 2016 Chapter 6: Iterators, Comprehensions, and Generators
Lead by: Tom Kono and Kevin Silverstein
Apr 8, 2016 Chapter 5: Functional Python
Lead by: Chaochih Liu and Paul Hoffman
Mar 25, 2016 Chapter 4: Object Oriented Python
Lead by: Skylar Wyant and Felipe Reyes