perl-Bio-SDRS - Perl extension for Sigmoidal Dose Response Search, a tool

Property Value
Distribution ALT Linux Sisyphus
Repository Autoimports noarch
Package name perl-Bio-SDRS
Package version 0.11
Package release alt1
Package architecture noarch
Package type rpm
Installed size 38.57 KB
Download size 38.57 KB
Official Mirror
Bio::SDRS implements the Sigmoidal Dose Response Search of assay responses
described in the paper by
Rui-Ru Ji, Nathan O. Siemers, Lei Ming, Liang Schweizer, and Robert E
The module is implemented using a simple object oriented paradigm
where the object stores all the information needed for a calculation
along with a state variable, `STATE'. The state variable has three
possible values, `'setup'', `'calculating'' and `'calculated''. The
value of `'setup'' indicates that the object is being setup with
data, and any results in the object are inconsistent with the data.
The value of `'calculating'' indicates the object's computations are
in progress and tells the code not to delete intermediate files. This
object runs in parallel, and the object destruction code gets called
when each thread exits. Intermediate files must be protected at that
time.  The value of `'calculated'' indicates that the object's
computational results are consistent with the data, and may be
returned to a calling program.
The `'calculate'' method is used to update all the calculated values
from the input data. It checks the state variable first, and only does
the calculation if the state is `'setup''. Once the calculations are
complete, then the state variable is set to `'calculated''. Thus, the
`calculate' method can be called whenever a calculated value is
needed, and there is no performance penalty.
The module initializes the `Bio::SDRS' object with a state of
`'setup''. Any data input sets the state to `'setup''. Any requests
for calculated data, calls `'calculate'', which updates the state
variable so futures requests for calculated data return quickly.
N.B. This module uses parallel programming via a fork call to get
high performance.  *You must close all database connections prior to
calling the `calculate' method, and reopen them afterwards. In
addition, you must ensure that any automated DESTROY methods take in
account their execution when the child processes terminated.*


Package Version Architecture Repository
perl-Bio-SDRS - - -


Name Value
/usr/bin/perl -
/usr/share/perl5 -
perl(Getopt/ -
perl( >= 0.450
perl(Math/ >= 5.0
perl( -
perl(Statistics/ >= 1.020
perl( -
perl( -
rpmlib(PayloadIsLzma) -


Name Value
perl(Bio/ = 0.110
perl(Bio/ -
perl-Bio-SDRS = 0.11-alt1


Type URL
Binary Package perl-Bio-SDRS-0.11-alt1.noarch.rpm
Source Package perl-Bio-SDRS-0.11-alt1.src.rpm

Install Howto

  1. Add the following line to /etc/apt/sources.list:
    rpm [Sisyphus] noarch autoimports
    rpm [Sisyphus] noarch autoimports
  2. Update the package index:
    # sudo apt-get update
  3. Install perl-Bio-SDRS rpm package:
    # sudo apt-get install perl-Bio-SDRS



See Also

Package Description
perl-Bio-SDRS-scripts-0.11-alt1.noarch.rpm Bio-SDRS scripts
perl-Bio-SFF-0.007-alt1.noarch.rpm Standard Flowgram Format for Perl
perl-Bio-SSRTool-0.04-alt1.noarch.rpm The great new Bio::SSRTool!
perl-Bio-SeqHash-0.1.4-alt1.noarch.rpm get one or more sequences from a FASTA file quickly
perl-Bio-SeqReader-0.1.3-alt2_9.noarch.rpm Class providing methods for representing header,
perl-Bio-Taxonomy-GlobalNames-0.07-alt1.noarch.rpm Perlish OO bindings to the L<Global Names Resolver|> API
perl-Bio-Tools-Alignment-Overview-0.36-alt1.noarch.rpm just another represetation for biological sequence alignment
perl-Bio-Tools-CodonOptTable-1.05-alt1.noarch.rpm A more elaborative way to check the codons usage!
perl-Bio-Tools-Primer3Redux-0.09-alt1.noarch.rpm BioPerl-based tools for Primer3 (redone)
perl-Bio-Tools-ProteinogenicAA-0.021-alt1.noarch.rpm A object list of proteinogenic amino acids
perl-Bio-Tools-Run-Qcons-0.112881-alt1.noarch.rpm perl module Bio-Tools-Run-Qcons
perl-Bio-Trace-ABIF-1.06-alt1.noarch.rpm Perl extension for reading and parsing ABIF (Applied
perl-Bio-Translator-0.6.1-alt1.noarch.rpm Translate DNA sequences
perl-Bio-Translator-scripts-0.6.1-alt1.noarch.rpm Bio-Translator scripts
perl-Bio-Util-AA-0.1.6-alt1.noarch.rpm Basic Amino Acid utilities