zenodo.md

Zenodo documentation

File size

According to Zenodo FAQ:

We currently accept up to 50GB per dataset (you can have multiple datasets); there is no size limit on communities.

So we don't expect much files to have an individual size above 50 GB.

API

REST API

The rate limit is

100 requests per minute, 5000 requests per hour

List of HTTP status codes

Example of direct API link for a given dataset: https://zenodo.org/api/records/8183728

Query

Search guide

Dataset examples

MD-related file types

Query:

resource_type.type:"dataset" AND filetype:"tpr"

Datasets:

• Simulations of a beta-2 adrenergic receptor monomer on a flat membrane
• GROMACS simulations of unfolding of ubiqutin in a strong electric field

zip files

Query:

resource_type.type:"dataset" AND filetype:"zip" AND (simulation* "molecular dynamics" gromacs charmm namd)

Datasets:

• All-atom molecular dynamics simulations of SARS-CoV-2 envelope protein E
• Structural dynamics of DNA depending on methylation pattern: Simulation dataset
• Exploring the interaction of a curcumin azobioisostere with Abeta42 dimers using replica exchange molecular dynamics simulations
• Molecular dynamics simulation data of regulatory ACT domain dimer of human phenylalanine hydroxylase (PAH) (with unbound ligand) (with multiple zip files)

Some dataset cannot be found with keywords. For instance:

• Ternary lipid composition in a curved geometry, more flat surface

Accessing zip file content

Zip file content can be obtained through a preview page provided by Zenodo.

Example dataset: All-atom molecular dynamics simulations of SARS-CoV-2 envelope protein E

• preview for NoPTM-2_Mix_CHARMM36m_0.1x3mks.zip
• preview for NoPTM-4_POPC_CHARMM36m_0.1x3mks.zip

Note that the preview is available for the first 1000 files only.

Zip files with tree-like structure

Some zip file content are really dense, with many folders and sub-folders.

Examples:

• In the dataset "Input files and scripts for Hamiltonian replica-exchange molecular dynamics simulations of intrinsically disordered proteins using a software GROMACS patched with PLUMED", a preview of the file hremd-idp.zip is available here.
• In the dataset "2DUV Machine Learning Protocol Code", a preview of the file code.zip is available here.

These complexe zip files are handled by the current implementation of the Zenodo crawler.

Issues with zip file content

Sometimes, zip file contents are not accessible.

Example dataset: G-Protein Coupled Receptor-Ligand Dissociation Rates and Mechanisms from tauRAMD Simulations

• preview not available for Example_b2AR-alprenolol.zip probably because file is too large (5.4 GB)