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 |