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My name is (Alexander) Niema Moshiri, and I am an Associate Teaching Professor in the Computer Science & Engineering Department at the University of California, San Diego. I work on computational biology, with a research focus on viral phylogenetics and epidemiology. I also place a heavy emphasis on teaching, namely on the development of online educational content, primarily Massive Adaptive Interactive Texts (MAITs). You can find more information about me on my website or in my Curriculum Vitae (CV).

Niema Moshiri's Projects

agc-virus-benchmark icon agc-virus-benchmark

Niema's benchmarking experiment of Assembled Genomes Compressor (AGC) on viral data

baidu-netdisk-cfg icon baidu-netdisk-cfg

Niema's scripts/notes for playing with the temporary *.baiduyun.uploading.cfg files that are created while files are being uploaded to Baidu Netdisk

bgtools icon bgtools

bgtools: A Python package for managing playing board games

biotenzar icon biotenzar

Bioinformatics Tools for the Tenzar Platform

bisb-bmi-handbook icon bisb-bmi-handbook

Handbook for the Bioinformatics & Systems Biology (BISB) and Biomedical Informatics (BMI) PhD programs at UC San Diego

bisb-website icon bisb-website

Stuff related to my work in updating the UCSD BISB program website

black-chocobo icon black-chocobo

Mirror of source code for Black Chocobo, by sithlord48 and vegetass4

coatran icon coatran

CoaTran: Coalescent tree simulation along a transmission network

cosmo icon cosmo

Source code from Ficedula's Cosmo editor (version 0.91)

data-structures-textbook icon data-structures-textbook

Repository for source code of the Data Structures online textbook (Niema Moshiri and Liz Izhikevich, 2016)

dual-birth-model icon dual-birth-model

Code and simulation data for "A two-state model of tree evolution and its applications to Alu retrotransposition"

favites icon favites

FAVITES (FrAmework for VIral Transmission and Evolution Simulation)

favites-covid-lite icon favites-covid-lite

A simplified (and much faster) simulation pipeline specifically for COVID-19 contact + transmission + phylogeny + sequence simulation

favites-lite icon favites-lite

FAVITES-Lite: A lightweight framework for viral transmission and evolution simulation

ff7-save-checksum icon ff7-save-checksum

Writes the correct checksum to every save slot in a Final Fantasy VII (PC?) save file

gamedb icon gamedb

Niema's databases for games from various consoles

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