Forum:help identifying bioinformatics operations tools

Question

[jsmedmar]

Regards,

I would like to tap into the Biostars community knowledge for a quick question. Please feel free to mark as out of scope if this type of questions are not allowed in Biostars (couldn't find the rules). We are trying to identify open source bioinformatics operations tools that provide support for databases (individuals, samples, NGS experiments, informatics apps, results), assets management (data import and storage), automated tool deployment (not necessarily execution), etc. So far we have identified the following:

• SeqWare
• QuickNGS
• OTP
• Genome Modeling System (GMS)
• GenomeVIP
• HTSFlow
• GenePattern

Do you guys know about more?

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Things we are not looking for:

• Domain Specific Workflow Languages / Specifications (e.g. CWL, WDL, BioDSL, NGLess, etc)
• Workflow Management Systems (e.g. Toil, Cromwell, bpipe, Cosmos, FireWorks, Kronos, Pegasus, etc)
• Application Suites (e.g. bcbio-nextgen, genPipes, OmicsPipe, ClusterFlow, etc)
• Server/Cloud Workbenches (e.g. DNANexus, Arvados, FireCloud, SevenBridges, Galaxy, Taverna, etc)

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Features we are interested in:

• Databasing of Patients, Samples, NGS Experiments, Bioinformatics Applications, Analyses Results, or more
• Comprenhensive RESTful API with documentation
• NGS Assets Management (Permissions, Storage, Tracking)
• Automated deployment and tracking of bioinformatics applications (agnostic to apps/languages/infrastructures/WMS etc)
• Operational automations on data import and analyses status change
• User Interface to browse and manage metadata and analyses results previews/visualization

Thanks again and sorry if question is out of scope.

By the way, we are aware of the following lists:

• https://github.com/pditommaso/awesome-pipeline
• https://github.com/common-workflow-language/common-workflow-language/wiki/Existing-Workflow-systems
• https://gist.github.com/danielepolencic/ef16bbc770129a60296503315a3b268f

[Ram]

Moved post to forum.

[jsmedmar]

Thanks, forum is a better place for this question

[GenoMax]

Basically you are looking for a NGS Laboratory Information Management system (LIMS). Open source/free?

Answer 1

[A. Domingues]

Miso-lims seems to be appropriate for your tasks:

Hence, we are developing MISO, an open-source LIMS for recording sequencing metadata. We are using freely available tools that are industry standard, well documented, and easy to set up on minimal hardware. As a bare system, MISO can store relevant metadata based on a wide array of NGS sequencing platforms (e.g. Illumina GA, HiSeq and MiSeq, Roche 454, ABI SOLiD and PacBio RS) and public repository data submission schemas (e.g. the Sequence Read Archive at the EBI), and has many features common to bespoke and proprietary LIMS, such as secure authentication, fine-grained access control, barcode tracking, and reporting.

source https://github.com/TGAC/miso-lims docs http://tgac.github.io/miso-lims/

[jsmedmar]

This is very nice! The documentation is very thorough. Yet, miso seems more suitable to groups actually running sequencing cores. We are looking for something more suited for groups running a Bioinformatics Core, where once data is retrieved from a Sequencing Core, a Data Repository or External Collaborators you can track and crunch that data in a systematic way

Answer 2

[peter.amstutz]

Maybe something like TranSMART https://transmartfoundation.org/scientists-clinicians/ for patient management and Arvados http://arvados.org for sequencing data management & analysis?

Answer 3

[Jeremy Leipzig]

Databasing of Patients, Samples, NGS Experiments, Bioinformatics Applications, Analyses Results, or more

yeah TransMart I2B2

Comprenhensive RESTful API with documentation

http://intermine.org ?

NGS Assets Management (Permissions, Storage, Tracking)

sounds LIMS-y

Automated deployment and tracking of bioinformatics applications (agnostic to apps/languages/infrastructures/WMS etc)

GA4GH Task Execution Schema (TES)

Operational automations on data import and analyses status change that's just CI/CD

User Interface to browse and manage metadata and analyses results previews/visualization

sounds like tableau/spotfire?

worth a read: https://www.biorxiv.org/content/biorxiv/early/2017/12/21/191783.full.pdf

Answer 4

[JC]

We cover all of that in our platform https://www.databiology.com/ let me know if you want to know more or a demo

[jsmedmar]

Hey Juan thanks for your response, I look at the databiology website and the descriptions are aligned with the question I asked. Although we are mostly interested in open source solutions might be a good idea to learn more about it. Let me know how to reach out for a demo!

[JC]

Hi, you can get access and more information here https://www.databiology.com/index.php/signup