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Martin Smith (mdsmith)

mdsmith

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Company:@PacificBiosciences

Location:Menlo Park, CA

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Martin Smith's repositories

MatMulLibCpp

OpenCL accelerated Matrix Multiply Library in C++

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MatMulLibPy

A library for fast Matrix Multiplication in Python, with OpenCL acceleration.

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CodonAligner-Validation

For testing and quantifying the advantages of a codon aligner in 454 sequences.

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dot_files

my very basic dot_files

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hyphy

HyPhy: Hypothesis testing using Phylogenies

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MLEpyOCL

using pyOpenCL to accelerate a model of MLE

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MulMulLibCpp

Multiple multiplication (e.g. exponentiation and maximum likelihood) library accelerated with OpenCL

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OCLHYPHY

OCL implementation of the maximum likelihood calculation.

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BasicFMAtest

Just a basic FMA4 test for our (and potentially your) FMA4 compatible systems (eg. Bulldozer, Interlagos...)

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bsrelBatchRunner

A python program to run BSREL on batches of input Nexus files utilizing bpsh and a cluster.

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BSRELvarSim

Simulation Study of BSRELvar

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CACL

Codon Aligner in OpenCL

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deepconsensus

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.

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DumbView

A PacBio genome browser for command line nerds

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FUBAR3Dsims

Simulation code (in HBL) for FUBAR3D

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IterOptBSREL

HyPhy batch files to iteratively optimize a BSREL model of sequence evolution

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ManuCollabTest

Manuscript writing collaboration test

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multiBSREL

A batch file for running BSREL, BSREL3 and MG94 quickly, easily, and comparably.

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oclCalcBench

A suite for testing and benchmarking various memory accession techniques in OpenCL

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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!

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pbdoctorb

PacBio data inspection/munging tools (unsupported)

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PRmm

PulseRecognizer minus minus

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pylagames

Misc games and AIs in Python

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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.

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PyTreeTools

Tree tools in Python

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pyxsd

Python Class Mappings for XML Schema

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RelaxedSim

Simulations!

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SeqChomp

Shortens the sequences in a Nexus file.

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simdjs_experimentation

Experimenting with SIMD.js

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ucsd-thesis

This is an effort to create the canonical LaTeX style for typesetting UCSD doctoral dissertations.

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