Owner

GLYCAM-Web

5 indexed repositories · View on GitHub

gmml
Glycam Molecular Modeling Library

C++ · 7 stars
website
A bare-bones repo to contain public website stuff and issues related to the GLYCAM Web Django apps.

HTML · 6 stars
gems
Glycam Extensible Modeling System

Python · 5 stars
MD_Utils

Shell · 2 stars
GLYCAM_Delegator_Docker
Standalone version of the molecular modeling engine used by GLYCAM-Web

Shell · 0 stars

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GP: Provide the user with the molecular weight of the protein and the molecular weight of the attached glycans Open

feature GMML Needs Design

GLYCAM-Web/website#19 · 4 comments · 1 reaction · 1 assignee · Indexed Sep 16, 2026
project.zip does not preserve symbolic links - might want to add project.tar Open

bug Needs Design

GLYCAM-Web/website#32 · 11 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
3D-SNFG in LiteMol bug. Name clash between PDB names and Glycam. SLB (Gal with 2,3,6 decoration) is shown as Purple Octagon, should be Yellow Circle according to glycam. Open

bug enhancement

GLYCAM-Web/website#34 · 3 comments · 0 reactions · 3 assignees · Indexed Sep 16, 2026
Carbbuilder should provide versions of the pdb files for download that do not contain hydrogens. Open

CB feature GEMS Needs Design

GLYCAM-Web/website#54 · 3 comments · 0 reactions · 3 assignees · Indexed Sep 16, 2026
Draw Glycan Open

call-for-comments feature GEMS Needs Design

GLYCAM-Web/website#70 · 2 comments · 0 reactions · 2 assignees · Indexed Sep 16, 2026
Phosphate notation Open

GLYCAM-Web/website#71 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Documentation for GlycoProtein submission Open

docs feature

GLYCAM-Web/website#82 · 2 comments · 0 reactions · 2 assignees · Indexed Sep 16, 2026
Prepush check for checking Docker image tag synchronization.md Open

feature Needs Design testing

GLYCAM-Web/website#111 · 0 comments · 0 reactions · 2 assignees · Indexed Sep 16, 2026
Grafting/Glyspec is broken Open

bug

GLYCAM-Web/website#129 · 2 comments · 0 reactions · 2 assignees · Indexed Sep 16, 2026
add link to this repo on our main site Open

enhancement feature

GLYCAM-Web/website#130 · 5 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
JSON API: the Marco and ListEntities services do not conform to schema Open

GLYCAM-Web/website#150 · 4 comments · 0 reactions · 4 assignees · Indexed Sep 16, 2026
Polybuilder allows me to build sequences that are impossible. Open

enhancement PB

GLYCAM-Web/website#156 · 5 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Errors during initial git ops should be fatal but aren't Open

bug

GLYCAM-Web/website#161 · 1 comment · 0 reactions · 5 assignees · Indexed Sep 16, 2026
Use of '-c agro' removes the environment file from the Slurm stack Open

bug

GLYCAM-Web/website#162 · 1 comment · 0 reactions · 2 assignees · Indexed Sep 16, 2026
Add a Ring conformation choice to the GAG builder on glycam.org Open

CB feature good first issue

GLYCAM-Web/website#167 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Website not working for some users. Open

bug

GLYCAM-Web/website#169 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Remove need for library to be in bin/ and lib/. Put library in lib/ only, use bin/ for executables Open

enhancement

GLYCAM-Web/gmml#112 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Consolidate/update parameter use in GMML Open

enhancement

GLYCAM-Web/gmml#115 · 1 comment · 0 reactions · 2 assignees · Indexed Sep 16, 2026
Issue with GAG parameters Open

bug

GLYCAM-Web/gmml#116 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Carbbuilder hangs on very large carbohydrate structures. Open

bug

GLYCAM-Web/gmml#121 · 0 comments · 0 reactions · 2 assignees · Indexed Sep 16, 2026
PDB2glycam formatted files available as an option from GlyFinder. Open

enhancement

GLYCAM-Web/gmml#124 · 0 comments · 0 reactions · 2 assignees · Indexed Sep 16, 2026
Sequences with unnecessary brackets do not fail well e.g. [LFucp[2Me,4A]a1-2]DGalpb1-OH Open

enhancement

GLYCAM-Web/gmml#135 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Add test that takes sequences, builds 3D structures, runs sugar ID and checks the sequences match the inputs. Open

enhancement

GLYCAM-Web/gmml#141 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Missing prep entries for metadata. Open

GLYCAM-Web/gmml#144 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Compiler segfaulting when compiling gmml Open

bug

GLYCAM-Web/gmml#145 · 5 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Derivatives to a 6 branch should remain rotatable when resolving overlaps, but should not show up as possible rotamers to user Open

bug

GLYCAM-Web/gmml#146 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 16, 2026
response.json in the build directory of a carbohydrate has a lot of null values Open

question

GLYCAM-Web/gmml#147 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Wrong error when C1 requested, but anomer is C2. Open

enhancement

GLYCAM-Web/gmml#149 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Clean Up Includes Open

enhancement

GLYCAM-Web/gmml#152 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
hooks wont run the most recent version Open

bug enhancement

GLYCAM-Web/gmml#153 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
GEMSHOME removal Open

bug enhancement

GLYCAM-Web/gmml#154 · 4 comments · 0 reactions · 2 assignees · Indexed Sep 16, 2026
Test number 016 fails to remain consistent between container and bare metal Open

bug

GLYCAM-Web/gmml#155 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Read/Write mol2 format files Open

enhancement

GLYCAM-Web/gmml#158 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Read/Write mmcif/pdbx files Open

enhancement

GLYCAM-Web/gmml#159 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Feature request: GMML error generator Open

enhancement

GLYCAM-Web/gmml#161 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 16, 2026
It's possible to build and get a minimized structure of DGlcpa1-1DGlcpa1-OH Open

bug

GLYCAM-Web/gmml#164 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Our approach to labelling residues and linkages doesn't work for ano-ano linkages Open

question

GLYCAM-Web/gmml#165 · 4 comments · 0 reactions · 2 assignees · Indexed Sep 16, 2026
Test 019 segfaults sometimes Open

bug

GLYCAM-Web/gmml#169 · 2 comments · 0 reactions · 2 assignees · Indexed Sep 16, 2026
KDO derivatives not working on test swarm Open

bug

GLYCAM-Web/gmml#170 · 1 comment · 0 reactions · 2 assignees · Indexed Sep 16, 2026
DFrupa2-1DFrupa2-OH breaks gmml. Open

bug

GLYCAM-Web/gmml#171 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
DKdopa2-OH does not build on test Open

bug

GLYCAM-Web/gmml#172 · 5 comments · 0 reactions · 2 assignees · Indexed Sep 16, 2026
Buttons and labels are looking messed up on actual Open

GLYCAM-Web/gmml#173 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Allowing for random placement of derivatives in each iteration of the repeat unit of a glycomaterial Open

GLYCAM-Web/gmml#176 · 0 comments · 0 reactions · 2 assignees · Indexed Sep 16, 2026
Bad links in publications Open

bug enhancement

GLYCAM-Web/website#174 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Legacy glycoprotein builder email has a bad link Open

bug

GLYCAM-Web/website#175 · 4 comments · 0 reactions · 3 assignees · Indexed Sep 16, 2026
Carbohydrate builder timeouts on large structures Open

bug CB

GLYCAM-Web/website#177 · 12 comments · 0 reactions · 3 assignees · Indexed Sep 16, 2026
MolStar and derivative groups Open

Molstar

GLYCAM-Web/website#181 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 16, 2026
LFucpa is identified as DArab Open

bug

GLYCAM-Web/website#188 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
User feedback: What derivatives are available is not obvious. Open

enhancement

GLYCAM-Web/website#191 · 1 comment · 0 reactions · 2 assignees · Indexed Sep 16, 2026
MolStar: Sulfate bonds are not visualized correctly. Open

enhancement Molstar

GLYCAM-Web/website#192 · 0 comments · 0 reactions · 2 assignees · Indexed Sep 16, 2026

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