Mathematical Modelling and

Synthetic Biology Lab



Bioinformatic software

  • Trimming algorithm (2016) Perl scripts to implement trimming algorithm for NGS Illumina amplicon data. Zucca S, Villaraggia M, Gagliardi S, Grieco G, Valente M, Cereda C, Magni P. "Methodologies for the reliable analysis of amplicon-based NGS data managing allele drop-out effects", BMC Bioinformatics (2016) (under revision).
  • PaPI (2014) A Machine Learning method to predict the impact of DNA mutations on the protein function. Combines Pseudo Amino Acid Composition (PseAAC), Polyphen2 and Sift to predict and score the functional effect of every human coding mutation such as those identified by NGS analysis (2014).
  • Differentiation (2011)  An add-on for Orange data mining software package that allows the analysis of stem cell differentiation data. It extends Orange by providing functionality to download temporal gene expression data from GEO, identify the most informative genes and construct a predictive model of the cells differentiation stage. For further details refer to: L. Zagar, F. Mulas, S. Garagna, M. Zuccotti, R. Bellazzi, and B. Zupan. Stage prediction of embryonic stem cell differentiation from genome-wide expression data. Bioinformatics (2011) 27(18): 2546-2553.
  • D2D sum (2011) Matlab files and data related to the paper "Summarizing Probe Intensities of Affymetrix GeneChip 3' Expression Arrays Taking into Account Day-to-Day Variability" by Magni et al. published on IEEE/ACM Transactions on Computational Biology and Bioinformatics (2011).
  • MassSpec (2010) For details see N. Barbarini and P. Magni. Accurate peak list extraction from proteomic mass spectra for identification and profiling studies. BMC Bioinformatics, 2010). Executable files for Windows and LINUX platforms are available.
  • MsPI (2009) MsPI is a software tool for protein identification from PMF data. It is described in A. Tiengo, N. Barbarini, S. Troiani, L. Rusconi and P. Magni. A Perl procedure for protein identification by Peptide Mass Fingerprinting. BMC Bioinformatics, 2009. Perl files are available.
  • Bayesian Network Wizard (see Ferrazzi et al., Bioinformatics, 2009) Compiled software and source files.
  • TimeClust (2008) A tool for clustering gene expression time series. It is described in P. Magni, F. Ferrazzi, L. Sacchi, and R. Bellazzi. TimeClust: a clustering tool for gene expression time series. Bioinformatics, 24:430--432, 2008. Executable files for Windows are available.

Mathematical Modelling software

  • TGI-simulator (2012) A tool for simulating the well-known Simeoni Tumor Growth Inhibition model. It is described in N. Terranova and P. Magni. "TGI-Simulator: A visual tool to support the preclinical phase of the drug discovery process by assessing in silico the effect of an anticancer drug. Computer Methods and Programs in Biomedicine, 105(2):162--174, 2012. doiI:10.1016/j.cmpb.2011.09.001.
  • PSS (2011) Population Smoothing Splines (PSS)  R software (for more details see Russu et al., IEEE Transactions on Biomedical Engineering, 2011)
  • Bayes Min Mod (2006) A tool used in P. Magni, G. Sparacino, R. Bellazzi, and C. Cobelli. Reduced sampling schedule for the glucose minimal model: importance of Bayesian estimation. Am. J. Physiol. Endocrinol. Metab., 290:E177--E184, 2006.

Synthetic Biology software

  • SequenceAlignment (2009): a simple tool (originally written in MATLAB) expressly designed for the quality control check of new BioBrick. It allows the user to align the results of the sequencing procedure with the aspected sequences built up assembling simple parts according to the rules of Standard Assembly (modality Compare Sequence/BioBrick ). It offers also the possibility of simply align two sequences (modality Compare two Sequences ). SequenceAlignment executable files for Windows platforms can be downloaded free of charge for non-prot institutions.