![]() ![]() The corrected data may be returned in a variety of formats including those used by metabolic flux analysis software such as 13CFLUX, OpenFLUX and 13CFLUX2. Before and after data correction, several checks can be performed to ensure accurate data. It allows the correction of large and heterogeneous MS datasets for the presence of naturally occurring stable isotopes, initial biomass and several mass spectrometry effects. This tool streamlines the transfer of data from extraction via correction tools to 13C-Flux software by processing MS data from stable isotope labeling experiments. Here we describe iMS2Flux, software developed to automate, standardize and connect the data flow between mass spectrometric measurements and flux analysis programs. In order to facilitate high-throughput metabolic flux analysis, the automation of multiple steps in the analytical workflow is necessary. Currently the processing of mass spectrometric data is time-consuming and error-prone requiring peak by peak cut-and-paste analysis and manual curation. Finally the MS data and the labeling information it contains have to be assembled into a data format usable by flux analysis software (of which several dedicated packages exist). However, before the mass spectrometric data can be used it has to be corrected for biases caused by naturally occurring stable isotopes, by the analytical technique(s) employed, or by the biological sample itself. The most common approach for determining intracellular metabolic fluxes is to utilize mass spectrometry in combination with stable isotope labeling experiments. When the CPAN module hasn't been able to install a module, I revert to the commandline.Metabolic flux analysis has become an established method in systems biology and functional genomics. There is actually a stronger version of that ( fforce) but there are cases where that's not the answer either. And, yes, force install doesn't always help. I've found most modules install using the CPAN modules but occasionally some don't. ![]() However, I am generally pleased with Strawberry Perl. But since you are using strawberry happily, there must be some tricks I donot know.Īctually, I said ". How do you resolve module installation problem using Strawberry? I was using CPAN module that comes together with Strawberry. It always failed this test or that test and even "force install" does not help. But installing modules such as DBD::Mysql became a daunting task for me and I never succeeded. ![]() I tried several times to switch to Strawberry Perl. Re^4: installing correct Par::Packer on ActivePerl 5.12.2 If it helps anyone, I'm currently using Strawberry Perl 5.12.0 and PAR::Packer 1.006 I recall spending some months following the bug reports quite closely and trying whatever patches became available on CPAN. The last ActivePerl version I have is 5.10.1 and I'm using XP. Well, I suppose everyone's experiences will differ. So I think I have to downgrade to ActivePerl v5.10.0. But it does not work on ActivePerl v5.10.1 and v5.12.2, two versions which ActiveState provides downloads on their websites. Re^3: installing correct Par::Packer on ActivePerl 5.12.2įinally, when I use ActivePerl v5.10.0, the Par::Packer works. That's odd, I have activeperl (v5.10.0) and whatever PAR::Packer version PPM gave me and I never had a problem so far (Windows XP 32 bit). I spent a very long time trying to get PAR::Packer to work under ActivePerl and finally gave up. Re^2: installing correct Par::Packer on ActivePerl 5.12.2 ![]()
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