The following codes are available for download that are developed by the Wang group and fellow collaborators. If any of the codes are utilized for published research, please use the citations provided. In order to receive the codes, you are required to provide your name, e-mail address, and institute. This information is for solely recording purposes. Once you fill out the code, an e-mail should automatically be generated and sent to the e-mail you have given. If you have any questions about the program or notice any errors please feel free to contact Dr. Jin Wang at firstname.lastname@example.org
5GB1 Reduced Metabolic Model
This is the flux balance model used in our recently published paper “Comparative study of oxygen-limited and methane-limited growth phenotypes of Methylomicrobium buryatense 5GB1,” BEJ 2020. The model contains 443 reactions and 403 metabolites and contains the primary carbon assimilation pathways for Methylomicrobium buryatense 5GB1.
Self-Calibrate Warping (SCW)
This is the trajectory/spectrum alignment algorithm published in paper “Self-Calibrated Warping for Mass Spectra Alignment”, Cancer Information, 2011, vol. 10: 65-82.Full-text of the paper is available here.
With recent advances in mass spectrometry (MS) technologies, it is now possible to study protein profiles over a wide range of molecular weights in small biological specimens. However, MS spectra are usually not aligned or synchronized between samples. To ensure the consistency of the subsequent analysis, spectrum alignment is necessary to align the spectra such that the same biological entity would show up at the same m/z value for different samples. Self-calibrated warping (SCW) algorithm was proposed to address some of the challenges associated with serum MS data alignment.Note that SCW is a general trajectory/spectrum alignment algorithm, which can be applied to align other spectra such as NIR, UV/Vis absorbance etc., as well as the time series of process variables in batch processes.
Citation: click here, then click “Cite”.
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