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@nysbc New York Structural Biology Center / SEMC

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    26 repositories

    • hq-appion-producer

      Public
      Fork of Appion that products tasks and submits them to HyperQueue instead of executing them directly.
      Python
      •2•0•0•0•Updated Jan 17, 2025Jan 17, 2025

    • hq-home

      Public
      The home directory of our HyperQueue service account. Contains scripts to start HyperQueue servers for motioncor2 and ctffind4.
      Shell
      •0•0•0•0•Updated Jan 16, 2025Jan 16, 2025

    • semcq-producer

      Public
      Fork of Appion that is refactored to queue work that can be processed by a semcq worker.
      Python
      •2•0•0•0•Updated Jan 14, 2025Jan 14, 2025

    • leginon

      Public
      Python
      •
      Apache License 2.0
      •1•0•0•0•Updated Dec 24, 2024Dec 24, 2024

    • appion-slurm

      Public
      Fork of Appion that consists of the minimum needed for everyday operations at SEMC.
      Python
      •2•0•0•0•Updated Dec 17, 2024Dec 17, 2024

    • nhc-debian

      Public
      Shell
      •
      Other
      •0•0•0•0•Updated Dec 3, 2024Dec 3, 2024

    • emhub

      Public
      Web application for monitor EM results
      Python
      •
      GNU General Public License v3.0
      •4•0•0•0•Updated Aug 23, 2024Aug 23, 2024

    • xmipp

      Public
      Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy.
      C++
      •
      GNU General Public License v3.0
      •15•0•0•0•Updated Jul 18, 2024Jul 18, 2024

    • xmippCore

      Public
      Core functions for Xmipp and sharing with other packages (like Scipion)
      C++
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Jul 16, 2024Jul 16, 2024

    • redmine2github

      Public
      Scripts to migrate redmine tickets to github issues
      Python
      •
      MIT License
      •20•0•0•0•Updated Mar 14, 2024Mar 14, 2024

    • leginon-tutorial

      Public
      Docker image for leginon with simulated data for tutorial purpose
      PHP
      •
      Apache License 2.0
      •0•1•0•0•Updated Jan 3, 2024Jan 3, 2024

    • ansible-role-nvidia-driver

      Public
      Fork of NVIDIA Ansible role w/ added support for Debian.
      Jinja
      •
      BSD 3-Clause "New" or "Revised" License
      •68•0•0•0•Updated Oct 23, 2023Oct 23, 2023

    • ptolemy

      Public
      Public release of Ptolemy package for automated targeting of Cryo-EM grids
      Jupyter Notebook
      •2•0•0•0•Updated Oct 6, 2023Oct 6, 2023

    • image-folder-shrink

      Public
      Data reduction script invoked by retentioner via the imshrink function.
      Python
      •0•0•0•0•Updated Apr 5, 2023Apr 5, 2023

    • tiltgroup-wrangler

      Public
      Python
      •0•0•0•0•Updated Jan 30, 2023Jan 30, 2023

    • SEMCf

      Public archive
      Python code facility monitor system (temperatures, etc).
      Python
      •0•0•0•0•Updated Sep 27, 2021Sep 27, 2021

    • appion-protomo

      Public archive
      A Docker-based distribution of Appion-Protomo.
      tomographycryoemcryoetprotomoalignment
      PHP
      •
      Apache License 2.0
      •4•11•5•0•Updated Oct 23, 2020Oct 23, 2020

    • topaz

      Public archive
      Pipeline for particle picking in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •65•0•0•0•Updated Sep 21, 2020Sep 21, 2020

    • SpotitonTR

      Public archive
      Code for Spotiton Time Resolve experiments
      C#
      •0•0•0•0•Updated Aug 20, 2019Aug 20, 2019

    • fscupload

      Public archive
      Use a Django web application to calculate a 3D Fourier shell correlation remotely.
      Python
      •
      MIT License
      •1•0•0•0•Updated Feb 11, 2019Feb 11, 2019

    • imod_singularity

      Public archive
      A singularity container for IMOD.
      Shell
      •1•0•0•1•Updated Aug 9, 2018Aug 9, 2018

    • singularity-centos7-cuda8

      Public archive
      0•0•0•0•Updated Jul 24, 2018Jul 24, 2018

    • motioncor2-docker

      Public archive
      Instructions for building a CUDA 8.0-enabled Docker container to run MotionCor2_1.1.0.
      Shell
      •0•0•0•0•Updated Jul 11, 2018Jul 11, 2018

    • Anisotropy

      Public archive
      These are programs that deal with anisotropy (both resolution and sampling)
      Python
      •
      MIT License
      •9•21•4•0•Updated Mar 16, 2018Mar 16, 2018

    • cuda

      Public archive
      Useful resources for learning CUDA and its Python variants.
      0•0•0•0•Updated Dec 14, 2017Dec 14, 2017

    • Tilted-Collection

      Public archive
      Tilted Single-Particle CryoEM Data Collection
      Python
      •0•0•0•0•Updated May 15, 2017May 15, 2017