Merge pull request #3 from CambridgeUniversityPress/jb

Website edits

content/index.md

@@ -13,7 +13,7 @@ featured_image: 'background.png'
 ## Why this book? 
 
 This book focuses on the _practical side_ of network science — **working with
-network data** — to provide a more practical guide for data scientists to use network science.
+network data** — to offer a useful guide for data scientists to use network science.
 
 We hope that this book can help researchers in day-to-day tasks, starting from
 the very act of conceptualizing networks through to sophisticated network
@@ -70,11 +70,13 @@ the fundamentals of network data.
 
 {{< /details >}}
 
-## Datasets and code
+## Resources
 
-### Focal networks
+### Datasets: Focal networks
 
+- [Readme](wwnd-readme.md)
 - [wwnd-focal-networks.zip](wwnd-focal-networks.zip)
 
+### Errata
 
-
+- [Errata](errata.md)

content/wwnd-readme.md

@@ -0,0 +1,148 @@
+FOCAL POINTS - Working with network data
+========================================
+
+Working with network data
+James Bagrow and Yong-Yeol Ahn
+2024
+
+https://cambridge.org/network-data
+
+Our book uses six *focal points*, real-world networks, as examples to
+illustrate common issues and practices. Here we provide these networks for you
+to download and use. Some networks come in multiple forms, such as both static
+and dynamic representations and many have attributes associated with the nodes
+or edges. Each network provided in GraphML and GML files; most libraries
+such as NetworkX and igraph support these formats.
+
+Below we discuss some specifics for each network. Please see our book for more
+information.
+
+
+
+Zachary Karate Club
+-------------------
+
+The famous Zachary Karate Club. This network represent members of a university
+martial arts club who interacted heavily outside the club, according to surveys
+gathered by Wayne Zachary during the early 1970s. This club had a disagreement
+and split into two groups, one following the club president and the other the
+club's karate instructor. This group information is available in the `group`
+node attribute. 
+
+Original data `karate.mtx` (retrieved 22 August 2022) available at:  
+https://www.cise.ufl.edu/research/sparse/matrices/Newman/karate
+
+Reference:
+W. W. Zachary, An information flow model for conflict and fission in small
+groups, Journal of Anthropological Research 33, 452-473 (1977).
+https://doi.org/10.1086/jar.33.4.3629752
+
+
+
+Plant-pollinator network
+------------------------
+
+A network where nodes are either plant or pollinator species and links exist
+only from plant to pollinator when field observations were made of that
+pollinator acting to pollinate that plant. Nodes are identified by species
+names. This network was collected from field observations conducted in Spain.
+
+Original data (network ID `M_PL_058`) (retrieved 22 August 2022) available at:
+https://www.web-of-life.es/
+
+Reference:  
+Bartomeus, I., Vilà, M. & Santamaría, L. Contrasting effects of invasive plants
+in plant–pollinator networks. Oecologia 155, 761–770 (2008).
+https://doi.org/10.1007/s00442-007-0946-1
+
+
+
+Developer collaboration network
+-------------------------------
+
+A network representing software developers contributing to open source projects
+hosted by IBM on the GitHub online development platform. Nodes represent
+developers (identified by their GitHub usernames) and links connect developers
+who have edited one or more source code files in common, a simple measure of
+collaboration. We treat the network as weighted by associating with each link a
+weight counting the number of files commonly edited by the two developers.
+
+The `dynamic` directory contains yearly snapshots of the network from 2013--2017.
+
+
+Original data (deposited 26 March 2019) available at:  
+https://doi.org/10.6084/m9.figshare.7893002.v1
+
+Reference:  
+Bagrow, J., Bollt, E. An information-theoretic, all-scales approach to
+comparing networks. Appl Netw Sci 4, 45 (2019).
+https://doi.org/10.1007/s41109-019-0156-x
+
+
+
+Flavor network
+--------------
+
+A network representing recipe ingredients and the flavor molecules they
+contain, extracted from food science reference texts. Nodes are identified with
+integers prepended with "i" if the node is an ingredient or "c" if it is a
+flavor chemical. Associated with each ingredient is its name and category.
+Associated with each chemical is its name and CAS number.
+
+The `backbone` directory contains the multiscale backbone (Ch. 10) visualized
+in the original reference and in Ch. 1.
+
+_Note_: 
+It was discovered by Augustine Koh ([email protected]) and Lav
+Varshney ([email protected]) that "Farnesol", a flavor compound, is present
+both as an ingredient (ID i339) and compound (ID c951). Thus, you may want to
+remove farnesol from the ingredient list and from the ingredient-compound
+network.
+
+Original data `ingr_comp.zip` and `flavor_network_backbone.zip` (retrieved 20
+October 2022) available at:
+https://yongyeol.com/2011/12/15/paper-flavor-network.html
+
+Reference:  
+Ahn, YY., Ahnert, S., Bagrow, J. et al. Flavor network and the principles of
+food pairing. Sci Rep 1, 196 (2011).
+https://doi.org/10.1038/srep00196
+
+
+
+Human Reference Interactome
+---------------------------
+
+A protein-protein interaction network derived from high-throughput assays.
+Nodes are represented by standardized IDs that can be connected to GENCODE gene
+annotation metadata.
+
+Original data `HuRI.tsv` (retrieved 22 August 2022) available at:  
+http://www.interactome-atlas.org/download
+
+Reference:  
+Luck, K., Kim, DK., Lambourne, L. et al. A reference map of the human binary
+protein interactome. Nature 580, 402–408 (2020).
+https://doi.org/10.1038/s41586-020-2188-x
+
+
+
+Malawi Sociometer Network
+-------------------------
+
+A face-to-face contact network between 86 individuals living in a rural village
+in Malawi.  Edge weights denote the number of contacts between individuals
+during the study.
+
+The `dynamic` directory contains the dynamic network stored as a multigraph.
+Note that the contact day has been renumbered compared to the original release
+to match the contact time.
+
+Original data `tnet_malawi_pilot.csv` (retrieved 22 August 2022) available at:  
+http://www.sociopatterns.org/datasets/contact-patterns-in-a-village-in-rural-malawi/
+
+Reference:  
+Ozella, L. et al., Using wearable proximity sensors to characterize social
+contact patterns in a village of rural Malawi, EPJ Data Science 10, 46 (2021).
+https://doi.org/10.1140/epjds/s13688-021-00302-w
+

hugo.toml

@@ -55,4 +55,4 @@ url = "/#why-this-book"
 name = "Resources"
 identifier = "resources"
 weight = 400
-url = "/#datasets-and-code"
+url = "/#resources"