Forum: help identifying bioinformatics operations tools
8
gravatar for jsmedmar
15 months ago by
jsmedmar80
jsmedmar80 wrote:

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 Biostarts (couldn't find the rules). We are trying to identify open source bioinformatics operations tools that provide support for databasing (individuals, samples, NGS experiments, informatics apps, results), assets management (data import and storage), automated tool deployemnt (not necesarilly 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?


❌ 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)

✅ 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:

ADD COMMENTlink modified 14 months ago • written 15 months ago by jsmedmar80
1

Moved post to forum.

ADD REPLYlink written 15 months ago by RamRS25k

Thanks, forum is a better place for this question

ADD REPLYlink written 15 months ago by jsmedmar80
1

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

ADD REPLYlink written 15 months ago by genomax78k
2
gravatar for A. Domingues
15 months ago by
A. Domingues2.2k
Dresden, Germany
A. Domingues2.2k wrote:

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/

ADD COMMENTlink written 15 months ago by A. Domingues2.2k

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

ADD REPLYlink modified 15 months ago • written 15 months ago by jsmedmar80
1
gravatar for peter.amstutz
15 months ago by
peter.amstutz300
peter.amstutz300 wrote:

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

ADD COMMENTlink written 15 months ago by peter.amstutz300
1
gravatar for Jeremy Leipzig
15 months ago by
Philadelphia, PA
Jeremy Leipzig19k wrote:

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

ADD COMMENTlink written 15 months ago by Jeremy Leipzig19k
1
gravatar for JC
15 months ago by
JC9.5k
Mexico
JC9.5k wrote:

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

ADD COMMENTlink written 15 months ago by JC9.5k

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!

ADD REPLYlink modified 15 months ago • written 15 months ago by jsmedmar80

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

ADD REPLYlink written 15 months ago by JC9.5k
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