Explore Training Materials



Welcome to the Training Resources section!

Here you can find training materials on a wide variety of topics from next generation sequencing (NGS) to molecular dynamics. Navigate through various topics on the left side of this page to find an appropriate course.
Course content ranges from short videos to PDF and PowerPoint files.

Looking for a particular topic that is not found here? Contact us and we will point you in the right direction.

Workshop

Related Events

Connectivity Map Workshop

Date: Tuesday, December 04, 2018
Location: Broad Institute, 415 Main St., Cambridge, MA 02142
Classification: Workshop

BioC 2019

Date: Tuesday, June 25, 2019
Location: Rockefeller University
Classification: Workshop

Related Code

Blender_PNG_from_X3D.py

Description: Imports a monochrome .x3d model into Blender and automatically generates a snapshot in .png format and exports a model in .stl format.

Blender_STL_Cleanup.py

Description: Imports a .wrl file into Blender, cleans the mesh, and exports .stl, .x3d, and .blend formats.

Blender_VRML_cleanup_ribbon.py

Description: Imports a .wrl model into Blender and cleans the mesh; exports a .x3d scene, and a model in .blend format. This script is used with molecular ribbon models generated in Chimera, using Chimera_Molecular.py

Blender_Blend_from_X3D Set.py

Description: Imports a generic .x3d into Blender and exports it in .blend format.

Blender_STL_to_X3D.py

Description: Imports a .stl model into Blender, recolors it, and exports in .x3d and .blend formats.

Blender_VRML_Cleanup.py

Description: Imports a .wrl model into Blender and cleans the mesh; exports a .x3d scene, and a model in .blend format. This script is used with molecular surface models generated in Chimera, using Chimera_Molecular.py

Chimera_Volumetric.py

Description: Using UCSF Chimera, generates isosurface meshes from volumetric data (e.g., microscopy image stacks). Outputs monochrome surface as .stl, and radial-colored surface as .wrl.

Chimera_Chem.py

Description: Using UCSF Chimera, generate color and monochrome versions of a small molecule in ball-and-stick, CPK, and stick variations. Models are optimized for 3D printing and exported as .wrl and .stl files.

Chimera_Molecular.py

Description: Using UCSF Chimera, generate several color and monochrome models from molecular data in variations of ribbon and surface structure. Models are optimized for 3D printing and exported as an .x3d scene.

cor_to_pdb.f90

Description: Reads a CHARMM formatted coordinate file and write a PDB formatted coordinate file.

pdb_to_charmm.f90

Description: Reads a PDB file in RCSB or VMD format and writes CHARMM formatted sequence and extended coordinate files.

splitpdb1.sh

Description: Splits a multi-molecular PDB file into individual files.

PrimerID pipeline

Description: Processes data produced using the PrimerID method for amplicon sequencing to generate viral population frequency tables for nucleotides and amino acids.