Bayesic Research

Plasma 6 widget displaying script output

info@bayesicresearch.org (Anthony Greenberg) — Fri, 05 Jun 2026 00:00:00 +0000

Displays output of user-defined shell scripts to the Plasma Task Manager

FASTA and FASTQ file manipulation tools

info@bayesicresearch.org (Anthony Greenberg) — Tue, 03 Mar 2026 00:00:00 +0000

Command line tools for simple operations on FASTA and FASTQ files

isoSeq read alignment quality control

info@bayesicresearch.org (Anthony Greenberg) — Tue, 03 Mar 2026 00:00:00 +0000

Identifying and fixing poorly aligned isoSeq read segments

Analyze FASTA alignments

info@bayesicresearch.org (Anthony Greenberg) — Wed, 05 Jul 2023 00:00:00 +0000

Estimating sequence diversity from sequence alignments

COVID-19 tracking

info@bayesicresearch.org (Anthony Greenberg) — Wed, 12 Apr 2023 00:00:00 +0000

I tracked local infection rate data during the COVID pandemic (between 2020 and 2022). I am saving the resulting page here as a historical record. I stopped updating this page on December 20, 2022 after Tompkins County stopped publishing daily data tables.

This page displays plots tracking COVID-19 data for Tompkins County, New York State, and the Finger Lakes region. I look at the number of tests performed and the number of confirmed positives. The data are downloaded from the New York State Department of Health, and are available here.The plots are interactive, hovering the mouse over them reveals available options to modify them and get more information about the underlying data. I update the plots daily.

Variant hashing

info@bayesicresearch.org (Anthony Greenberg) — Tue, 11 Apr 2023 00:00:00 +0000

Fast locus similarity (LD) estimates using hashing

MCMC samplers

info@bayesicresearch.org (Anthony Greenberg) — Mon, 15 Feb 2021 00:00:00 +0000

Markov chain Monte Carlo samplers

Matrix operations

info@bayesicresearch.org (Anthony Greenberg) — Wed, 10 Feb 2021 00:00:00 +0000

A collection of matrix operations

Numerical Utilities

info@bayesicresearch.org (Anthony Greenberg) — Fri, 05 Feb 2021 00:00:00 +0000

Collection of numerical utilities

Site update

info@bayesicresearch.org (Anthony Greenberg) — Thu, 21 Jan 2021 00:00:00 +0000

When I first set up this here outfit more than five years ago, I needed to quickly set up a website to advertise myself. At the time, I heard about Squarespace from their ads on some podcasts I was listening to. It fit the bill perfectly: nice clean design templates, analytics displayed in a well-designed iOS app, e-mail service through Google, simple to add markdown content, no need for CSS coding. I have been with them ever since and have had zero complaints about the service itself. It has been rock stable, too.

align2bed

info@bayesicresearch.org (Anthony Greenberg) — Wed, 13 Jan 2021 00:00:00 +0000

Extract SNPs from alignments

BayesLiDiCal

info@bayesicresearch.org (Anthony Greenberg) — Wed, 13 Jan 2021 00:00:00 +0000

Bayesian analyses of limited dilution assays

GWA likelihood methods

info@bayesicresearch.org (Anthony Greenberg) — Wed, 13 Jan 2021 00:00:00 +0000

Likelihood methods for genome-wide associations

MuGen

info@bayesicresearch.org (Anthony Greenberg) — Wed, 13 Jan 2021 00:00:00 +0000

Multitrait genetic hierarchical models

Extract Polymorphic and Divergent Sites

info@bayesicresearch.org (Anthony Greenberg) — Tue, 12 Jan 2021 00:00:00 +0000

Extract polymorphic and divergent sites from alignments and VCF files

MuGaMix

info@bayesicresearch.org (Anthony Greenberg) — Tue, 12 Jan 2021 00:00:00 +0000

Multivariate Gaussian mixture models

Sample SNPs

info@bayesicresearch.org (Anthony Greenberg) — Tue, 12 Jan 2021 00:00:00 +0000

Uniform online sampling of SNP records from files

Status Bar for dwm

info@bayesicresearch.org (Anthony Greenberg) — Tue, 12 Jan 2021 00:00:00 +0000

Status bar for the dynamic window manager

Switching to Linux

info@bayesicresearch.org (Anthony Greenberg) — Mon, 01 Apr 2019 00:00:00 +0000

I have been using Apple computers close to full time since mid-90’s. Originally because I used Photoshop extensively for processing confocal microscope images and Macs were the standard platform for that. It helped that they were also relatively safe from viruses and generally stable. I switched to more computational work in the early 2000’s, and Apple was right there with Mac OS X, which still is a great interface to a Unix-like system. I have owned an Apple laptop continuously since around 2000.

There is more than one way to be a scientist

info@bayesicresearch.org (Anthony Greenberg) — Mon, 13 Aug 2018 00:00:00 +0000

There is a fascinating discussion happening on science twitter about what it means to be a scientist. It boils down to the question: is science just another job or is it some higher calling that demands total dedication? My colleague Lyza Maron wrote a particularly clear and compelling argument for the former. She gets at the crux of the problem here:

But if I was not doing science, and I did not even miss it, was I not a scientist anymore? Then who was I? It was a crisis of loss of identity that became evident every time I met someone new and they asked “What do you do?”

I think there are two somewhat separate sides to being a scientist. One is a set of mental habits and the other is a job description. A scientific mindset involves critically evaluating all information and making decisions using data, logic, and the scientific method. Individuals can use these habits of mind in everyday life whether they also work as a scientist in a lab or not. In this sense, changing jobs should not lead to a crisis of identity.

Power and limitations of genetics as a tool to study racial differences

info@bayesicresearch.org (Anthony Greenberg) — Tue, 03 Apr 2018 00:00:00 +0000

The recent New York Times opinion piece by the geneticist David Reich on genetics of differences between human races has generated much discussion among my scientist friends. It was followed by a rebuttal from 67 scholars of diverse backgrounds, and a sympathetic article by the blogger and essayist Andrew Sullivan. I typically stay away from this topic because given its horrific history it deserves vary careful treatment by experts in a variety of disciplines. I am not well equipped to discuss most aspects of this, but it did strike me that a few key points are either missing in the debate or scattered across the various contributions. I will attempt to collect and lay out the most essential arguments here. I will confine myself to a fairly narrow scope, in order to not stray beyond my area of expertise. Truth be told, I am writing this to some extent in order to clarify my own thinking, but I hope it will help others as well.

Fast ordered sampling of SNPs from large files

info@bayesicresearch.org (Anthony Greenberg) — Tue, 21 Nov 2017 00:00:00 +0000

Ever since I left my academic position and became independent, I have been interested in the idea of using minimal computer resources to perform big-data statistical analyses. I do not have a permanent office, so the only computer I own is a laptop, although it is a close to maximal-spec 15-inch MacBook Pro (mid-2015). I can use Amazon’s AWS for really big jobs, but the necessity to quickly trouble-shoot software and pipelines remains.

Accidental benchmarking of Apple's new file system, APFS

info@bayesicresearch.org (Anthony Greenberg) — Fri, 27 Oct 2017 00:00:00 +0000

Apple recently released High Sierra, the new version of Mac OS. While it is billed as one of those “stability releases” with few user-facing changes, it introduces a new file system, APFS. This system has already been rolled out for iOS devices. This is not something users interact with directly, but Apple lists a number of features (such as on-disk system snapshots) that are enabled by APFS.

Coincidentally, I have been working on a method to randomly sample records from files. High Sierra has become available in the middle of the project, while I was repeatedly benchmarking my code. I will report the details of the method soon (watch this space!). To test a base-line method, I wrote a program (in C++, compiled with Apple’s llvm with -O3 optimization) that reads a line of the target file and then probabilistically decides whether it will save it to an output file or not. The files can be text or binary. Given that the sampling is reasonably sparse, the execution is dominated by file reading operations. Binary files are read with the read() ifstream method, while text files are processed with an overload of the getline() function. I then use the clock() function to time execution. I vary the number of records sampled, and perform 15 replicates to estimate execution time variability, which can be due to any number of factors. For example, since I execute the program on my laptop other processes running at the same time can interfere by commandeering file I/O facilities.

The Google diversity memo makes an important mistake

info@bayesicresearch.org (Anthony Greenberg) — Thu, 10 Aug 2017 00:00:00 +0000

The recently-published memo (full text can be found at the end of this article) from a Google employee about the causes of gender disparity in the number of people working at the company generated a lively discussion. The arguments are as wide-ranging as the original post and involve many important topics. Given my area of expertise, I want to focus on a fairly narrow but fundamental part of the case made by the memo’s author. He summarizes it as follows:

Quickly extracting SNPs from alignments

info@bayesicresearch.org (Anthony Greenberg) — Fri, 19 May 2017 00:00:00 +0000

Working on a Drosophila population genetics project, I needed to extract SNPs from a large-ish data set of sequence alignments from the Drosophila Genome Nexus. The alignments are in a slightly strange but handy format: each line and chromosome arm is in a separate file. The sequences are all on one line in FASTA format, but with no traditional FASTA header. I needed 283 lines plus the D. simulans outgroup. I decided to come up with a way to do the SNP extraction on my laptop in reasonable time, and save to a popular (at least in quantitative genetics) BED format used by plink. Briefly, this SNP table format uses two bits to represent a genotype (since there are only four states: reference, alternative, heterozygote, or missing) and therefore is really compact.

Democratic turn-out in the 2016 election

info@bayesicresearch.org (Anthony Greenberg) — Fri, 11 Nov 2016 00:00:00 +0000

The unexpected election of Donald Trump as the next President of the United States has generated an avalanche of articles and social media posts attempting to explain what went wrong and why the pre-election predictions were so off. This event seems of a piece with the earlier similarly unexpected (based on polling) votes for Britain to leave the EU and Colombia to scuttle the peace deal with the FARC guerrillas. Much of the commentary has thus been focused on explaining the poll failure and on the possible motivations of Trump voters. Commentators typically use exit polls and percentages of the vote won by the candidates to bolster their arguments. When we look at the fraction of votes received, however, we are looking at a ratio of two quantities. Changing either the numerator or the denominator can change the value of the ratio. Might a separate examination of the changes in the number of votes won by each party tell us something about what happened? I started thinking about this after one of my friends shared a Twitter post comparing the Democratic turnout in the three latest elections. This quick analysis only looked at aggregate national numbers, an approach that likely obscures important patterns.

Inaugural post

info@bayesicresearch.org (Anthony Greenberg) — Fri, 28 Aug 2015 00:00:00 +0000

After about 20 years in academic science (25 if you count volunteering in a lab as an undergrad), I finally decided to go my own way. My academic career path has been unorthodox up to now, and I have been lucky to have the support of great advisers along the way. However, the mismatch between what I want to do and what is valued for the purposes of academic career advancement has become impossible to ignore. So instead of struggling to reconcile the incompatible I decided to try a different approach.