Software

Curvature Calculation Program
CCP, the “Curvature Calculation program”, analyses the curvature of single protofilaments (PFs) at the ends of microtubules (MTs) or sets thereof (up to 1000 PFs simultaneously).
To analyze fine details of the shape of experimental and theoretical PFs we have designed software called the “Curvature Calculation Program” or CCP (McIntosh et al., Cell 2008). CCP is written with Borland Delphi 7 medium for MS Windows 98 or higher, and it does not require any additional computer programs. Intel Pentium4 3000 MHz, AMD Athlon64 3200+ or newer processors are recommended. The program uses text files with the coordinates of the PFs, either acquired by tracing of the electron microscopic images with IMOD or as an output from numerical model calculations. The program window opens such files by showing all or a subset of the PFs selected by a user. The user can use mouse to move PFs relative to each other and organize them in groups (Fig. 1, PFs shown in blue in the left graph of the window). The selected group (Fig. 1, PFs in green) can then be used to calculate the shape of average PF (shown in red with error bars), as well as to view the local curvature of individual PFs in this group and their averages (green and red traces respectively in the graph on the right). These results can be saved in an output text file, if necessary. CCP calculates average PF shape for a selected group of PFs by computing the mean and its deviation for horizontal (X) and vertical (Z) coordinates within a user-defined segment, starting from (0,0); analogous procedures are then carried out for segments that are shifted by a user-defined step until reaching the end of the longest PF in this group. We routinely calculated the average shape for a group of 40-50 PFs, using the segments with 10-20 coordinates and step size 1. Local curvature of a segment of the PF was calculated with a least-squares method that uses arcs with variable radii to achieve the best fit to the PF segment of the user-defined size. The inverse value of this radius was used as a curvature for this PF segment. All values for the local PF curvatures cited in this paper were calculated as above but then adjusted so that they represent the angular deviation between two adjacent, linear segments 8 nm long (therefore, measured in degrees per dimer length). Finally, the CCP was used to calculate the orientation angles for the PF segments at a given distance from the MT wall (0,0). Such a distance interval is specified by a user, then the program uses a least-squares method to calculate the linear segment that fits best the selected PF segment. The angle between this linear segment and the horizontal axis is then calculated.

 

Figure 1. Screen Shot of the controls for the CCP program. For analysis and comparison, all PFs from a given class of MTs, e.g., KMTs from an early anaphase PtK1 cell as shown here were extracted as 2D points by the howflared program in IMOD and displayed on a single frame of reference. The PFs could then be sorted, either manually or by some objective criterion like the average orientation of their segment for a chosen distance from the MT wall, e.g. 6 – 12 nm, and then considered groups. Local curvature as a function of distance from the MT wall was computed and displayed (green lines, central panel) with mean values and standard deviations in a different color (red). Mean positions with their deviations (left panel, red) could also be displayed. The identifiers of all PFs from the original tomogram were preserved, so members of any given class could then be extracted as image files from the original tomograms.

For Windows OS. Manual included. ccp.zip (400 KB)

Blood Coagulation Model

Program for the solution of a complex mathematical model of blood coagulation published in (Panteleev et al. Biophys J 2006; 90(5): 1489-1500). Homogeneous and reaction-diffusion simulation of clotting is possible. For Windows OS. With manual. Bcm.rar (1 MB)

Software and protocols for Clot Growth Assay (CGA) and Thrombin/Fibrin Generation Assay (the list is under construction, April 2nd, 2009)

(Disclaimer: the information on this page is intended for reference only. All downloadable software is for reference only. There is no guarantee implied about the functionality of the software and protocols. Use this page at your own risk. However, we will be happy to answer all relevant research-related requests about our published Clot Growth and Thrombin/Fibrin Generation experiments. Please use the contact information posted on this website.)

Part I: Thrombin and Fibrin Generation Assay (in microplates)

  1. A set of OriginPro scripts and templates for automatic processing of Thrombin and Fibrin Generation Microplate Experiments (by Mikhail V Ovanesov, ovanesov@gmail.com) Download zipped archive with scripts and templates here: 041003_TG_templates_samples.zip (127 KB)
  2. Instructions for OriginPro Templates for the Thrombin Generation Assay. Download Word documentProtocol_processing.doc (35 KB)
  3. A protocol for thrombin and fibrin generation assay using microplate reader. Download Word documentThrombin_Generation_protocol_00_part_1.doc (57 KB)

Part II: Clot Growth Assay (videomicroscopy-based)

  1. A set of OriginPro scripts and templates for automatic processing of Clot Growth Experiments (by Mikhail V Ovanesov, ovanesov@gmail.com) Download zipped archive with scripts and templates here:041003_CG_templates_samples.zip (132KB)
  2. Clot growth image processing software Shoot (by Mikhail V Ovanesov, ovanesov@gmail.com) Download zipped archive with executable program here: Shoot09.84h(Eng)(nodriver)(exe)_.zip (260KB)
  3. Video capture software for clot growth experiments (by Andrey Baranov) Download zipped archive with executable program here: dscap.zip (334KB)
  4. Full protocol for clot growth experiment and processing: Download .txt file here:clot_growth_processing_protocol_parts_III_11.txt (34 KB)
  5. Troubleshooting: installation of video capture drivers Download .txt file here: how_to_install_driver.txt (1 KB)