PMID- 31208323
OWN - NLM
STAT- MEDLINE
DCOM- 20190806
LR  - 20200419
IS  - 1471-2105 (Electronic)
IS  - 1471-2105 (Linking)
VI  - 20
IP  - 1
DP  - 2019 Jun 17
TI  - Laboratory information management software for engineered mini-protein 
      therapeutic workflow.
PG  - 343
LID - 10.1186/s12859-019-2935-x [doi]
LID - 343
AB  - BACKGROUND: Protein based therapeutics are one of the fastest growing classes of 
      novel medical interventions in areas such as cancer, infectious disease, and 
      inflammation. Protein engineering plays an important role in the optimization of 
      desired therapeutic properties such as reducing immunogenicity, increasing 
      stability for storage, increasing target specificity, etc. One category of 
      protein therapeutics is nature-inspired bioengineered cystine-dense peptides 
      (CDPs) for various biological targets. These engineered proteins are often 
      further modified by synthetic chemistry. For example, candidate mini-proteins can 
      be conjugated into active small molecule drugs. We refer to modified 
      mini-proteins as "Optides" (Optimized peptides). To efficiently serve the 
      multidisciplinary lab scientists with varied therapeutic portfolio research goals 
      in a non-commercial setting, a cost effective extendable laboratory information 
      management system (LIMS) is/was needed. RESULTS: We have developed a LIMS named 
      Optide-Hunter for a generalized engineered protein compounds workflow that tracks 
      entities and assays from creation to preclinical experiments. The implementation 
      and custom modules are built using LabKey server, which is an Open Source 
      platform for scientific data integration and analysis. Optide-Hunter contains a 
      compound registry, in-silico assays, high throughput production, large-scale 
      production, in vivo assays and data extraction from a specimen-tracking database. 
      It is used to store, extract, and view data for various therapeutics projects. 
      Optide-Hunter also includes external processing stand-alone software 
      (HPLCPeakClassifierApp) for automated chromatogram classification. The 
      HPLCPeakClassifierApp is used for pre-processing of HPLC data prior to loading to 
      Optide-Hunter. The custom implementation is done using data transformation 
      modules in R, SQL, javascript, and java and is Open Source to assist new users in 
      customizing it for their unique workflows. Instructions for exploring a deployed 
      version of Optide-Hunter can be found at 
      https://www.labkey.com/case%20study/optide-hunter CONCLUSION: The Optide-Hunter 
      LIMS system is designed and built to track the process of engineering, producing 
      and prioritizing protein therapeutic candidates. It can be easily adapted and 
      extended for use in small or large research laboratories where multidisciplinary 
      scientists are collaborating to engineer compounds for potential therapeutic or 
      protein science applications. Open Source exploration of Optide-Hunter can help 
      any bioinformatics scientist adapt, extend, and deploy an equivalent system 
      tailored to each laboratory's workflow.
FAU - Brusniak, Mi-Youn
AU  - Brusniak MY
AUID- ORCID: 0000-0003-3950-1614
AD  - Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, 
      USA. mbrusnia@fredhutch.org.
FAU - Ramos, Hector
AU  - Ramos H
AD  - Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, 
      USA.
FAU - Lee, Bernard
AU  - Lee B
AD  - LabKey Software, 617 Eastlake Ave E #400, Seattle, WA, 98109, USA.
FAU - Olson, James M
AU  - Olson JM
AD  - Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, 
      USA.
LA  - eng
GR  - S10 OD020069/OD/NIH HHS/United States
PT  - Journal Article
DEP - 20190617
PL  - England
TA  - BMC Bioinformatics
JT  - BMC bioinformatics
JID - 100965194
RN  - 0 (Proteins)
MH  - Automation
MH  - Humans
MH  - Information Management
MH  - *Laboratories
MH  - *Protein Engineering
MH  - Proteins/*therapeutic use
MH  - *Software
MH  - User-Computer Interface
MH  - Workflow
PMC - PMC6580487
OTO - NOTNLM
OT  - HPLC/UPLC peak classification
OT  - LabKey software
OT  - Laboratory information management system
OT  - Protein engineering
OT  - Therapeutic protein
COIS- None.
EDAT- 2019/06/19 06:00
MHDA- 2019/08/07 06:00
PMCR- 2019/06/17
CRDT- 2019/06/19 06:00
PHST- 2019/01/16 00:00 [received]
PHST- 2019/06/05 00:00 [accepted]
PHST- 2019/06/19 06:00 [entrez]
PHST- 2019/06/19 06:00 [pubmed]
PHST- 2019/08/07 06:00 [medline]
PHST- 2019/06/17 00:00 [pmc-release]
AID - 10.1186/s12859-019-2935-x [pii]
AID - 2935 [pii]
AID - 10.1186/s12859-019-2935-x [doi]
PST - epublish
SO  - BMC Bioinformatics. 2019 Jun 17;20(1):343. doi: 10.1186/s12859-019-2935-x.