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Table 1 Five open source Analysis Information Management Systems (AIMS) compared across 5 categories: (1) metadata capabilities, (2) support for assets management, (3) features for systematic data processing, (4) mechanisms for results retrieval, and (5) availability and codebase status

From: Isabl Platform, a digital biobank for processing multimodal patient data

Challenge Feature Isabl GMS SeqWare QuickNGS HTS-flow
Metadata capabilities Metadata infrastructure Relational database, RESTful API + Swagger docs Relational database Relational database, RESTful API + online docs Relational database Relational database
Data model (ID system) Individuals
Samples
Experiments
(See Fig. 1)
Individuals
Samples
Experiments
(UUIDs)
Individuals
Samples
Experiments
(User Defined)
Experiments
(User Defined)
Experiments
(User Defined)
Metadata ingestion Excel batch, Web Forms, REST API Command line
Client
Web Form, CLI batch CSV batch SMITH LIMS integration
Assets management Data import CLI batch CLI one by one CLI batch and web Manual symlink LIMS integration
Reference data import Genomes, BED files, Arbitrary resources Genomes, variation lists, Ensembl Download scripts for public databases Genomes download
Data multimodality
Data organization Hash-based directory structure UUID based directory structure S3 buckets, user defined locations
Data processing Apps included
New Apps registration Python class Perl components Java components Shell scripts R modules
WMS (Deployment Support) WMS Agnostic (Local, LSF)* Custom WMS (LSF, OpenLava) Pegasus, Oozie (SGE, AWS) Shell scripting (SLURM) Custom WMS (SGE)
Operational automations Signals, Project Level auto-merge CRON Jobs
Results accessibility Software development kit Python package Perl library
Data provisioning CLI, file system, download CLI, file system CLI, file system, download Download CLI, file system, R objects
Purpose of user interface Metadata search and ingestion, status monitoring, results access Metadata search, status monitoring, results access Metadata search and ingestion, status monitoring Metadata search, end-user access to results Metadata search, apps deployment and configuration
Availability and codebase quality Availability Docker compose, PyPi (300 MB) Vagrant VM (200 GB) Vagrant VM (2 GB) Manual Install (4 MB) Manual Install (1 MB)
Last Commit (Github Stars) 2019 2015 (65) 2016 (26) Last release 2016 2016 (1)
Continuous integration
Docs status
Programming Languages Python, Vue, Javascript Perl, Ruby Java, JavaScript Bash, PHP PHP, R, JavaScript