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SOFTWARE AND DATA
Research on Complex Networks
Algorithm to perform a box covering using MEMB algorithm in C.
See enclosed "readme.txt" file for instructions.
Algorithm to calculate the fractal dimension of a network. This file includes MEMB,
CBB and random covering algorithms for Python. This package requires networkx. See file header for comments on how to use it.
In our papers we usually refer to a number of real-life networks, which we have collected
from various sources. The following table provides a short description of these databases,
where the number of nodes and links refers ONLY to the largest connected cluster.
| Short Name |
Number of nodes N |
Number of links L |
Description |
Link |
| Metabolic (E.coli) | 2859 | 6890 | Interactions between the metabolites of
E.coli in the course of the metabolic cycle
| Barabasi homepage
| | PIN yeast | 777 | 1797 | High-confidence filtered data for interactions between proteins in yeast
| M.Vidal homepage
| | PIN H.sapiens | 425 | 612 | Protein interactions in homo-sapiens
| CCSB Interactome Database
| | Protein homology | 30727 | 1206654 | Similarity between two proteins using the BLAST algorithm
| LGL homepage
| | Taxonomy | |
| | WWW | 325729 | 1090108 | Linked WWW pages in the nd.edu domain
| Barabasi homepage
| | Internet(routers) | 284772 | 449228
| | DIMES | 20612 | 60653 | Internet connections at the Autonomous System
level, as found by the DIMES project
| DIMES homepage
| | IMDB | 374510 | 15014833 | Co-appearance of actors in the same movie
| Barabasi homepage
| | Blogs | 200316 | 700737 | Links between blogs in the Sina blogosphere (http://blog.sina.com.cn)
| Paper by Fu et al.
| | HEP citations | 34401 | 420784 | High Energy Particle Physics citations from
the hep-th section of arxiv.org
| Pajek homepage
| | Cond-mat co-authorship | 15081 | 52582 | Two authors are connected if they have
collaborated in cond-mat papers
| | Guestbook signing | 19215 | 54623 | Links between users of the pussokram.com
online community that have signed guestbooks of other users
| Liljeros paper
| | Hospitals | 291295 | 10118441 | Contact network of patients hospitalized
in Sweden
| Liljeros paper
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Research on Cities
- Download datasets we used in our research on the
City Clustering Algorithm (CCA) and population growth.
- Dataset for USA in ascii format. Also available in Excel format here.
- Dataset for GB for years 1981 and 1991.
- Dataset for population of USA MSAs.
- Dataset for boundaries of USA MSAs in 2000.
- Dataset for population of USA Places in 2000.
- Dataset regarding boundaries for Places or FIPS are too large. We make it available under request
or they can be downloaded directly from the US Census Bureau.
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Download results obtained with the CCA algorithm in the USA and GB.
- Download FIPS corresponding to each CCA cluster, using the CCA algorithm, for l=2,3,4,5km.
- Download FIPS corresponding to each MSA.
- Download MSA/CCA correspondence.
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CCA algorithm code: Coming soon in C/C++ and Python.
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Research on the phase diagram for jammed matter
Algorithm and simple instruction to the simulation of
preparing the jammed packings. This file includes the Distinct Element
Method (DME) for Fortan. See
detailed instruction for comments on how to use it.
- Download datasets we used in our research on the
the phase diagram. The data contains the box size of the system, the coordination for each particle in the system and the force between any two touched particles.
- Dataset for RCP line in the phase diagram. The instruction for reading the data here.
- Dataset for RLP line in the phase diagram. The instruction for reading the data here.
- Dataset for G line in the phase diagram. The instruction for reading the data here.
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Research on the entropy for jammed matter
Algorithm to the simulation
of preparing the jammed packings and the calculation of the entropy
from the packings. See instruction
for comments on how to use it.
- Download datasets we used in our research on the
the entropy for different friction coefficient.
- Dataset for friction coefficient 0.00001.
- Dataset for friction coefficient 0.05.
- Dataset for friction coefficient 0.1.
- Dataset for friction coefficient 0.2.
- Dataset for friction coefficient 0.3.
- Dataset for friction coefficient 0.5.
- Dataset for friction coefficient 1.
- Dataset for friction coefficient 10000.
- Origin files for all the datasets.
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Research on generating sequences of long-range correlations (in 1D and 2D)
This tar file contains the program to generate long-range correlations in 1d and 2d. The method is explained in the paper: H. A. Makse, S. Havlin, M. Schwartz, and H. E. Stanley, Method
for Generating Long-Range Correlations for Large Systems, Phys. Rev.
E 53, 5445-5449 (1996).
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