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  • 1
    Electronic Resource
    Electronic Resource
    Potential use of measurements of callus and male gametophyte NaCl tolerance in lucerne breeding (1989)
    Springer
    Euphytica 43 (1989), S. 245-251 
    Details
    ISSN: 1573-5060
    Keywords: Medicago sativa ; lucerne ; alfalfa ; callus culture ; pollen ; salt tolerance ; in vitro selection
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary Relationships between whole-plant and germination NaCl tolerance and two in vitro measures of NaCl tolerance were evaluated in lucerne (Medicago sativa L.). No significant correlations were observed between relative NaCl tolerance of non-regenerating callus cultures, herbage regrowth, seed or pollen germination, and pollen tube growth. Simulated selection using indirect measures of NaCl tolerance produced small expected gains in relative NaCl tolerance during herbage regrowth and seed germination. These gains were less than 30% of those expected with direct selection for regrowth or germination tolerance. Selection based on the apparent NaCl tolerance of callus tissue or male gamephytes would appear unproductive. Direct selection for NaCl tolerance both at germination and during mature plant regrowth would appear to be necessary to rapidly develop lucerne populations with field-relevant levels of tolerance to NaCl stress.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00023059
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    Some practical aspects of computer applications in a fermentor hall (1983)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 25 (1983), S. 809-844 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The use of computers in a fermentation pilot plant is described from a practical point of view. The aim is not the application of a computer to a single special process but a general application of computers to prepare and present data for the following analysis of fermentation processes. The hardware is normally bought from computer manufacturers, but some additional installations are useful. Application software has to be developed by the biotechnologist, therefore the software structure is the most important part of the computer application. Data storage is divided into three parts: short-time memory, long-time storage, and a medium memory mainly to be used in process analyses and process control. Four types of programs are used: main schedule tasks, low-priority on-line tasks, sense-switch routine, and different off-line programs. A table of all programs is presented, the main schedule task is described in detail to demonstrate the software structure.
    Additional Material: 13 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bit.260250316
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  • 3
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    Chlorophyll a in Antarctic sea ice from historical ice core data (2012)
    Wiley
    Details
    Publication Date: 2012-11-10
    Description: Sea ice core chlorophyll a data are used to describe the seasonal, regional and vertical distribution of algal biomass in Southern Ocean pack ice. The Antarctic Sea Ice Processes and Climate – Biology (ASPeCt – Bio) circumpolar dataset consists of 1300 ice cores collected during 32 cruises over a period of 25 years. The analyses show that integrated sea ice chlorophyll a peaks in early spring and late austral summer, which is consistent with theories on light and nutrient limitation. The results indicate that on a circum-Antarctic scale, surface, internal and bottom sea ice layers contribute equally to integrated biomass, but vertical distribution shows distinct differences among six regions around the continent. The vertical distribution of sea ice algal biomass depends on sea ice thickness, with surface communities most commonly associated with thin ice (
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 4
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    VCF-Miner: GUI-based application for mining variants and annotations stored in VCF files (2016)
    Oxford University Press
    Details
    Publication Date: 2016-03-17
    Description: Next-generation sequencing platforms are widely used to discover variants associated with disease. The processing of sequencing data involves read alignment, variant calling, variant annotation and variant filtering. The standard file format to hold variant calls is the variant call format (VCF) file. According to the format specifications, any arbitrary annotation can be added to the VCF file for downstream processing. However, most downstream analysis programs disregard annotations already present in the VCF and re-annotate variants using the annotation provided by that particular program. This precludes investigators who have collected information on variants from literature or other sources from including these annotations in the filtering and mining of variants. We have developed VCF-Miner, a graphical user interface-based stand-alone tool, to mine variants and annotation stored in the VCF. Powered by a MongoDB database engine, VCF-Miner enables the stepwise trimming of non-relevant variants. The grouping feature implemented in VCF-Miner can be used to identify somatic variants by contrasting variants in tumor and in normal samples or to identify recessive/dominant variants in family studies. It is not limited to human data, but can also be extended to include non-diploid organisms. It also supports copy number or any other variant type supported by the VCF specification. VCF-Miner can be used on a personal computer or large institutional servers and is freely available for download from http://bioinformaticstools.mayo.edu/research/vcf-miner/ .
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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  • 5
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    The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation (2014)
    Oxford University Press
    Details
    Publication Date: 2014-06-27
    Description: Motivation:  The Biological Reference Repository (BioR) is a toolkit for annotating variants. BioR stores public and user-specific annotation sources in indexed JSON-encoded flat files (catalogs). The BioR toolkit provides the functionality to combine and retrieve annotation from these catalogs via the command-line interface. Several catalogs from commonly used annotation sources and instructions for creating user-specific catalogs are provided. Commands from the toolkit can be combined with other UNIX commands for advanced annotation processing. We also provide instructions for the development of custom annotation pipelines. Availability and implementation: The package is implemented in Java and makes use of external tools written in Java and Perl. The toolkit can be executed on Mac OS X 10.5 and above or any Linux distribution. The BioR application, quickstart, and user guide documents and many biological examples are available at http://bioinformaticstools.mayo.edu . Contact: Kocher.JeanPierre@mayo.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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