Fig 1.
Flowchart for the use of SEDFIT in command line operation with a secondary software.
The secondary software organizes access control and preprocesses data. After SEDFIT is spawned by the secondary program, it reads a specifically formatted input file, and provides a graphical user interface with options controlled by the secondary program. Upon termination of SEDFIT analysis, its output files are read, and quality control, postprocessing and documentation by the secondary program can take place. This flow allows a single or multiple copies of SEDFIT to be utilized solely as a computational module within a framework of the secondary program, which may enforce GMP compatibility, incorporate results into meta-analyses, and/or provide an expert system or AI for automated analysis and quality control.
Table 1.
Input parameters will be read from a file named as third command line parameter. It is in xml format and parameters are case sensitive. An example can be found in S1 File.
Table 2.
List of Additional Output Parameters.
Output will be written in an xml formatted file in the designated output folder. Output parameters include the same parameters regarding data, model, and solution conditions as the input parameters, but also include the additional parameters in this table.
Fig 2.
Sedimentation analysis of a stressed NISTmAb sample at 50,000 rpm and 20°C using the command line operation of SEDFIT.
Top: Scan files and best fit (for clarity, showing black dots only for every 2nd data point of every 2nd scan) with a c(s) model automatically converged to a final rmsd of 0.006743 OD (colored lines). Progression of scan time is indicated by color from purple to red. Middle and Bottom: Residuals bitmap and residuals overlay. Plot was made using the software GUSSI [59], which is spawned from the script mlSEDFIT.
Fig 3.
Comparison of c(s) distributions computed with the command line initialization of SEDFIT and with manual operation.
The distribution from command line operation (Fig 2), and exhibits a monomer peak at 6.477 S with 29.20% of signal, a trace degradation product at 4.199 S with 0.95% of signal, a dimer peak at 9.473 S with 12.51% of signal, and higher aggregates with collective sw 16.799 S and 51.77% of signal. The analogous manually operated analysis producing a monomer peak at 6.481 S with 29.27% of signal, a degradation product of 4.178S with 0.92% of the signal, a dimer peak at 9.488 S with 12.51% of signal, and higher aggregates with collective sw of 16.81 S with 51.73% of signal. Integration and plot were made using the software GUSSI [59], which can be spawned from the script mlSEDFIT.
Fig 4.
Example for postprocessing of results from SEDFIT analysis in mlSEDFIT.
The output generated through the command line interface can be read in the mlSEDFIT script. For example, integration of distribution peaks can be carried out in this script after mouse clicks on the peaks in the distribution plot, as shown.