This file contains 16 monolayer networks and 16 multilayer networks. You can download it directly.

Contents:
+---monolayer
|       911.gml
|       Club.gml
|       DMLC.gml
|       Dolphins.gml
|       Eron.gml
|       Escherichia.gml
|       Football.gml
|       Game of Thrones.gml
|       Jazz.gml
|       Lesmis.gml
|       NEUSNCP.gml
|       NS.gml
|       Polbooks.gml
|       Power.gml
|       USAir.gml
|       Voles.gml
|
\---multilayer
    |   USAir.gml
    |
    +---BOS
    |       .DS_Store
    |       BOS.edges
    |       bos_genetic_layers.txt
    |       bos_genetic_nodes.txt
    |
    +---Candida
    |       .DS_Store
    |       Candida.edges
    |       candida_genetic_layers.txt
    |       candida_genetic_nodes.txt
    |
    +---CElegans
    |       .DS_Store
    |       CElegans.edges
    |       celegans_connectome_layers.txt
    |       celegans_connectome_nodes.txt
    |       celegans_genetic_layers.txt
    |       celegans_genetic_nodes.txt
    |
    +---CKM
    |       CKM-Physicians-Innovation_nodes.txt
    |       CKM.edges
    |       CKM_layers.txt
    |
    +---DanioRerio
    |       .DS_Store
    |       DanioRerio.edges
    |       danioRerio_genetic_layers.txt
    |       danioRerio_genetic_nodes.txt
    |
    +---EUAirTransportation
    |       EUAirTransportation.edges
    |       EUAirTransportation_layers.txt
    |       EUAirTransportation_nodes.txt
    |
    +---Gallus
    |       .DS_Store
    |       Gallus.edges
    |       gallus_genetic_layers.txt
    |       gallus_genetic_nodes.txt
    |
    +---HepatitusCVirus
    |       .DS_Store
    |       HepatitusCVirus.edges
    |       hepatitusC_genetic_layers.txt
    |       hepatitusC_genetic_nodes.txt
    |
    +---HumanHerpes4
    |       .DS_Store
    |       HumanHerpes4.edges
    |       humanHerpes4_genetic_layers.txt
    |       humanHerpes4_genetic_nodes.txt
    |
    +---LondonTransport
    |       LondonTransport.edges
    |       london_transport_disruptions_summary.txt
    |       london_transport_layers.txt
    |       london_transport_nodes.txt
    |       london_transport_raw.edges
    |
    +---Oryctolagus
    |       .DS_Store
    |       Oryctolagus.edges
    |       oryctolagus_genetic_layers.txt
    |       oryctolagus_genetic_nodes.txt
    |
    +---Padgett
    |       Padgett-Florentine-Families_layers.txt
    |       Padgett-Florentine-Families_nodes.txt
    |       Padgett.edges
    |
    +---Plasmodium
    |       .DS_Store
    |       Plasmodium.edges
    |       plasmodium_genetic_layers.txt
    |       plasmodium_genetic_nodes.txt
    |
    +---Rattus
    |       .DS_Store
    |       Rattus.edges
    |       rattus_genetic_layers.txt
    |       rattus_genetic_nodes.txt
    |
    \---Xenopus
            .DS_Store
            Xenopus.edges
            xenopus_genetic_layers.txt
            xenopus_genetic_nodes.txt

Usage: 
1. Monolayer networks
        All of the provided monolayer network datasets are in .gml format. If you are using Python, you can load the dataset via NetworkX library, as followings:

import networkx as nx

G = nx.read_gml('911.gml')
print(nx.info(G))

2. Multilayer networks
        The 9 multilayer networks are placed in 9 folders, repectively. There are three files in each folder, with *.edges represents the edges in multilayer networks, *_layers.txt represents the layers' infomation and *_nodes.txt shows the nodes' labels. Muxviz can be employed to plot multilayer networks.

 *.edges file format:
node1 layer1 node2 layer2 weight (optional)
node1 layer1 node2 layer2 weight (optional)

e.g.,

1 1 1 1 1
1 1 2 1 1
1 1 10 1 1
1 1 12 1 1
...

1 physical_association
2 direct_interaction
3 colocalization
4 association
...

1 vpr
2 SF3B2
3 tat
4 CCNT1
...