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biojava

BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.

bootcamp-programming

The in-class programming project for QBC Bootcamp

cet_toolbox

common-pubs

UCSF Physical Underpinnings of Biological Systems 2015

cryodrgn

Neural networks for cryo-EM reconstruction

cwf_denoise

explain-embed

Jupyter notebook explaining low-dimensional embeddings

init_tomo

introcv

jce

Structure alignment and analysis using BioJava

lui

Laser User Interface

mdscale

A free and open-source Multidimensional Scaling (MDS) library for Java.

mxe

MXE (M cross environment)

nccb_website

website for Northern California Computational Biology group

numba

NumPy aware dynamic Python compiler using LLVM

numlockx

Unofficial mirror of the numlockx code

occupy

offlineimap

Read/sync your IMAP mailboxes [Python]

opentrack

Head tracking software for MS Windows, Linux, and Apple OSX

pdbmunger

Tools for robust manipulation of PDB files

posters

Refereed posters

ptui

Phenotypic Training User Interface

pubs-analysis

pyem

Python programs for electron microscopy

pyem-nb

Practical pyem through Jupyter notebooks

qdrec

Quantal Dose Response Calculator

relion

Image-processing software for cryo-electron microscopy

relion-external

Programs for Relion's "External" job interface

restore

A CNN for denoising cryo-EM images

sfsuxmas

Automatically exported from code.google.com/p/sfsuxmas