This document examines how to use RELION 4.0 (beta2 as of writing) with Warp 1.09 and M 1.09 for single particle analysis.
Special thanks to Alister Burt, Pranav Shah and Dimitry Tegunov for discussion on this Twitter thread.
We use the RELION tutorial dataset (beta-galactosidase collected on JEOL CRYO ARM 200, a subset of EMPIAR-10204).
| import numpy as np | |
| def sigmoid(x): | |
| return 1 / (1 + np.exp(-x)) | |
| def neural_network(X, y): | |
| learning_rate = 0.1 | |
| W1 = np.random.rand(2, 4) | |
| W2 = np.random.rand(4, 1) |
| #!/usr/bin/env bash | |
| set -Eeuo pipefail | |
| trap cleanup SIGINT SIGTERM ERR EXIT | |
| script_dir=$(cd "$(dirname "${BASH_SOURCE[0]}")" &>/dev/null && pwd -P) | |
| usage() { | |
| cat <<EOF | |
| Usage: $(basename "${BASH_SOURCE[0]}") [-h] [-v] [-f] -p param_value arg1 [arg2...] |
| /* BoxNet2D runner | |
| * Based on Warp 1.0.7 by Dimitry Tegunov https://github.com/cramerlab/warp/ | |
| * Command line interface and Linux port by @biochem_fan | |
| * Licensed under GPLv3 | |
| */ | |
| using System; | |
| using System.IO; | |
| using System.Linq; // for toList() | |
| using System.Diagnostics; // for Stopwatch |
| # atom2svg.py by @biochem_fan | |
| # VERSION: 210224 | |
| # License: GPLv2 or later (ask me if this is inconvenient for you) | |
| # | |
| # LIMITATIONS: | |
| # - This supports only a single chain. If you have more chains, shift residue IDs and merge chains. | |
| # | |
| # TODO: | |
| # - Residue numbers (how to pack??) | |
| # |
| #!/bin/bash | |
| if [[ ! -d 3DEM ]] | |
| then | |
| mkdir 3DEM | |
| fi | |
| cd 3DEM | |
| curl -s http://mail.ncmir.ucsd.edu/pipermail/3dem/ |\ |
| """ | |
| Script to convert eman2 segmentation hdf maps to imod model files at a user defined contour level. | |
| Requires python>=3.5 as well as having Eman2 and IMOD in the path. | |
| Usage: `python3 tomoseg_to_imod.py -i EXAMPLE.hdf -o EXAMPLE.mod -t 0.8` | |
| Author: Benjamin Barad <[email protected]> | |
| """ | |
| import argparse |
| escape_char / | |
| comment_char % | |
| % This file was generated by taking the LC_TIME section from en_US and | |
| % replacing date/time representation with that of sv_SE from the glibc | |
| % locale sources | |
| % (http://sourceware.org/git/?p=glibc.git;a=tree;f=localedata/locales;hb=HEAD) | |
| % (https://www.gnu.org/software/libc/manual/html_node/Formatting-Calendar-Time.html) | |
| % This file is part of the GNU C Library and contains locale data. |
| ;;; emacs-zotero-bib-fetch.el --- Manage Zotero collections from emacs | |
| ;; | |
| ;; Filename: emacs-zotero-bib-fetch.el | |
| ;; Author: Anders Johansson, based on zotelo by Spinu Vitalie | |
| ;; Maintainer: Anders Johansson | |
| ;; Copyright (C) 2011-2014, Anders Johansson and Spinu Vitalie | |
| ;; Created: 1 Jul 2014 | |
| ;; Version: 1.2 | |
| ;; URL: https://github.com/andersjohansson/emacs-zotero-bib-fetch | |
| ;; Keywords: zotero, emacs, reftex, bibtex, bibliography manager |
If you were to give recommendations to your "little brother/sister" on things that they need to do to become a data scientist, what would those things be?
I think the "Data Science Venn Diagram" (http://drewconway.com/zia/2013/3/26/the-data-science-venn-diagram) is a great place to start. You need three things to be a good data scientist:
