Scalpel pipeline

Scalpel specifications


Unique identifier OMICS_05395
Name Scalpel
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Perl
Computer skills Advanced
Version 0.5.4
Stability Stable
Maintained Yes



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  • person_outline Giuseppe Narzisi <>

Publications for Scalpel

Scalpel citations

PMCID: 4404262

[…] possible by host and location, were dissected for quantitative pcr (qpcr) analysis by removal and collection of the capitulum and the anterior portion of the scutum. separate sterile forceps and scalpel blades were used for the dissection of each tick. for mosquitoes and march flies, tissue from the head, abdomen and thorax was extracted. tick tissue was pooled in groups of 1–10 samples […]

PMCID: 4640359

[…] the membrane filters were fixed with 100 % v/v methanol and stained with 0.05 % v/v crystal violet dye (sigma-aldrich, australia). the membranes were carefully removed from the insert using a scalpel blade and mounted onto glass slides. the number of migrated cells per insert (10 fields were chosen from each insert) was counted using the m2 program of the micro-computer imaging […]

PMCID: 4285754

[…] day after transferred to dishes. the test was performed in triplicate and each biological replicate was performed using 50 such seed., seeds were peeled off the hulls and cut longitudinally with a scalpel. the half-seeds were soaked in a 0.2% solution of ttc at 28°c for 2 h in the dark, and then rinsed with distilled water until the water ran clear. the seeds were then observed under a light […]

PMCID: 3444268

[…] variation between two measurements of a population of nuclei was ~3%. the different nuclei populations were measured for 10,000 nuclei., embryos were isolated from the endosperm using a sharp scalpel blade, immediately frozen in liquid nitrogen, and then stored at –80 °c. for each extract, 30 embryos were ground in liquid n2, and total rna was extracted by a hot phenol procedure according […]

Scalpel institution(s)
Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Stony Brook University, Stony Brook, NY, USA; New York Genome Center, New York, NY, USA; Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Mexico; Columbia University Medical Center, New York, NY, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
Scalpel funding source(s)
Supported by grants from the US National Institutes of Health (R01-HG006677 and U01- CA168409) and the US National Science Foundation (DBI-1350041) and by grants from the Cold Spring Harbor Laboratory (CSHL) Cancer Center Support (5P30CA045508), the Stanley Institute for Cognitive Genomics and the Simons Foundation (SF51 and SF235988).

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