mdsmith

@PacificBiosciences Menlo Park, CA

Pinned Repositories

CodonAligner-Validation
For testing and quantifying the advantages of a codon aligner in 454 sequences.
Language:Python1 2 00
dot_files
my very basic dot_files
Language:Shell1 2 00
hyphy
HyPhy: Hypothesis testing using Phylogenies
Language:C++1 2 00
MatMulLibCpp
OpenCL accelerated Matrix Multiply Library in C++
Language:C++22
MatMulLibPy
A library for fast Matrix Multiplication in Python, with OpenCL acceleration.
Language:Python2 3 02
MLEpyOCL
using pyOpenCL to accelerate a model of MLE
Language:Python1 2 01
MulMulLibCpp
Multiple multiplication (e.g. exponentiation and maximum likelihood) library accelerated with OpenCL
Language:C++1 2 01
OCLHYPHY
OCL implementation of the maximum likelihood calculation.
Language:C++1 2 01
OCLhyphyTree
OpenCL implementation of HYPHY's Maximum Likelihood loops
Language:C++1 2 01
ScreenSpin
A fun shell script for checking whether or not you are in an instance of GNU Screen
Language:Shell1 2 00

mdsmith's Repositories

mdsmith/MatMulLibCpp
OpenCL accelerated Matrix Multiply Library in C++
Language:C++22
mdsmith/MatMulLibPy
A library for fast Matrix Multiplication in Python, with OpenCL acceleration.
Language:Python2 3 02
mdsmith/CodonAligner-Validation
For testing and quantifying the advantages of a codon aligner in 454 sequences.
Language:Python1 2 00
mdsmith/dot_files
my very basic dot_files
Language:Shell1 2 00
mdsmith/hyphy
HyPhy: Hypothesis testing using Phylogenies
Language:C++1 2 00
mdsmith/MLEpyOCL
using pyOpenCL to accelerate a model of MLE
Language:Python1 2 01
mdsmith/MulMulLibCpp
Multiple multiplication (e.g. exponentiation and maximum likelihood) library accelerated with OpenCL
Language:C++1 2 01
mdsmith/OCLHYPHY
OCL implementation of the maximum likelihood calculation.
Language:C++1 2 01
mdsmith/BasicFMAtest
Just a basic FMA4 test for our (and potentially your) FMA4 compatible systems (eg. Bulldozer, Interlagos...)
Language:C++2 0
mdsmith/bsrelBatchRunner
A python program to run BSREL on batches of input Nexus files utilizing bpsh and a cluster.
Language:Python2 0
mdsmith/BSRELvarSim
Simulation Study of BSRELvar
Language:Python2 0
mdsmith/CACL
Codon Aligner in OpenCL
Language:C++2 02
mdsmith/deepconsensus
DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.
mdsmith/DumbView
A PacBio genome browser for command line nerds
Language:Python1 0
mdsmith/FUBAR3Dsims
Simulation code (in HBL) for FUBAR3D
Language:Python2 0
mdsmith/IterOptBSREL
HyPhy batch files to iteratively optimize a BSREL model of sequence evolution
1
mdsmith/ManuCollabTest
Manuscript writing collaboration test
2 0
mdsmith/multiBSREL
A batch file for running BSREL, BSREL3 and MG94 quickly, easily, and comparably.
mdsmith/oclCalcBench
A suite for testing and benchmarking various memory accession techniques in OpenCL
2 0
mdsmith/oclCopyBench
A suite for testing and benchmarking various methods of getting data from host to device. I'm going to go crazy and put reading and writing from device memory in here too. Wow!
Language:C++2 0
mdsmith/pbdoctorb
PacBio data inspection/munging tools (unsupported)
Language:Python1 0
mdsmith/PRmm
PulseRecognizer minus minus
Language:Python1 0
mdsmith/pylagames
Misc games and AIs in Python
Language:Python1 0
mdsmith/pysam
Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.
Language:C1 0
mdsmith/PyTreeTools
Tree tools in Python
Language:Python2 0
mdsmith/pyxsd
Python Class Mappings for XML Schema
Language:Python2 0
mdsmith/RelaxedSim
Simulations!
2 0
mdsmith/SeqChomp
Shortens the sequences in a Nexus file.
Language:Python2 0
mdsmith/simdjs_experimentation
Experimenting with SIMD.js
2 0
mdsmith/ucsd-thesis
This is an effort to create the canonical LaTeX style for typesetting UCSD doctoral dissertations.
Language:TeX2 0