BioFabric-users

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Hi! If you have a hairball network that you want to comb, this is the place to be. Please feel free to post all your questions, feedback, tips, and commentary about BioFabric (www.BioFabric.org) here in the BioFabric-users group.

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Ivan Swart, Bill Longabaugh6

2/9/17

Preparing data in R

I have posted some (pretty crude) R code as a gist on GitHub that should get you started: https://

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Preparing data in R

I have posted some (pretty crude) R code as a gist on GitHub that should get you started: https://

2/9/17

Tom Roth, Bill Longabaugh2

9/27/16

Names drop in RBioFabric output

If node zone labels get too tiny, I found that they can have trouble getting rendered. What happens

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Names drop in RBioFabric output

If node zone labels get too tiny, I found that they can have trouble getting rendered. What happens

9/27/16

Robert Flight, Bill Longabaugh4

9/4/15

running on linux??

Excellent! If you have any questions, post here or email me. Best wishes, Bill On Friday, September 4

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running on linux??

Excellent! If you have any questions, post here or email me. Best wishes, Bill On Friday, September 4

9/4/15

Todd Detwiler, William Longabaugh5

9/12/14

The BioFabric Demo

Nothing like having a potential user to kick me into action! I have hacked away at the Super-Quick

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The BioFabric Demo

Nothing like having a potential user to kick me into action! I have hacked away at the Super-Quick

9/12/14

nomesh gopalani, Bill Longabaugh2

3/6/14

How to save a image in BioFabric (empty output JPEG file)?

A few things to try: 1) I don't recommend using the JPG format; the PNG format is much better for

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How to save a image in BioFabric (empty output JPEG file)?

A few things to try: 1) I don't recommend using the JPG format; the PNG format is much better for

3/6/14

Moussa Mansour, William Longabaugh2

2/20/14

Time Complexity

The default layout is just breadth-first search, so that should theoretically be O(v+e). But there is

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Time Complexity

The default layout is just breadth-first search, so that should theoretically be O(v+e). But there is

2/20/14

bifx...@gmail.com, William Longabaugh4

9/18/13

Java 7 and biofabric

Isabelle: The behavior you are describing is for the rubber-box drag selection, which highlights

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Java 7 and biofabric

Isabelle: The behavior you are describing is for the rubber-box drag selection, which highlights

9/18/13

Nilanjan Bhattacharya, William Longabaugh2

9/3/13

help with using biofabric

Sorry for the delay in replying. I've been out of the office for the last week. Four things

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help with using biofabric

Sorry for the delay in replying. I've been out of the office for the last week. Four things

9/3/13

Nilanjan Bhattacharya, William Longabaugh3

7/20/13

making sense of the fabric

One thing about the World Bank example: that is a case where, by design, the edge wedge shapes do

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making sense of the fabric

One thing about the World Bank example: that is a case where, by design, the edge wedge shapes do

7/20/13

wayne mitchell, William Longabaugh2

6/6/13

general instruction reference on network visualisation

Wayne: Thanks! I actually haven't read it, but I've heard a couple good things about the book

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general instruction reference on network visualisation

Wayne: Thanks! I actually haven't read it, but I've heard a couple good things about the book

6/6/13

Bill Longabaugh, bifx...@gmail.com3

5/28/13

New BioFabric Demo Written in D3

Thanks! You're right, it would be a great way to explain shadow links. I'm adding that to my

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New BioFabric Demo Written in D3

Thanks! You're right, it would be a great way to explain shadow links. I'm adding that to my

5/28/13

Julius Christopher Barsi, William Longabaugh2

2/25/13

SIF Pd relationship (Activator AND Repressor?)

Julius: You could specify PdA and PdR as the relationship tags. Visually, they would not look any

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SIF Pd relationship (Activator AND Repressor?)

Julius: You could specify PdA and PdR as the relationship tags. Visually, they would not look any

2/25/13

Bill Longabaugh

2/7/13

New Blog Post on BioFabric

There is a nice new blog post on BioFabric by Tanya Jeffries at The Graph Enthusiast: http://http://

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New Blog Post on BioFabric

There is a nice new blog post on BioFabric by Tanya Jeffries at The Graph Enthusiast: http://http://

2/7/13

Bill Longabaugh

2/1/13

New BioFabric Network Posted Online!

Doug Burke has posted a BioFabric network of the tweets from the 221st meeting of the American

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New BioFabric Network Posted Online!

Doug Burke has posted a BioFabric network of the tweets from the 221st meeting of the American

2/1/13

11/12/12

Running Multiple Simultaneous Instances of BioFabric on a Mac

It turns out there is a shortcoming with the downloadable, standalone BioFabric executable for the

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Running Multiple Simultaneous Instances of BioFabric on a Mac

It turns out there is a shortcoming with the downloadable, standalone BioFabric executable for the

11/12/12

11/12/12

Layout Using Node Attributes

The "Layout Using Node Attributes" feature is the way that the user can explicitly specify

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Layout Using Node Attributes

The "Layout Using Node Attributes" feature is the way that the user can explicitly specify

11/12/12

wlong...@systemsbiology.org

11/9/12

Enabling Shadow Links

Shadow Links, which are described in the BMC paper (see Figure 2), are really useful for getting a

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Enabling Shadow Links

Shadow Links, which are described in the BMC paper (see Figure 2), are really useful for getting a

11/9/12

wlong...@systemsbiology.org, Daniel Baker3

11/9/12

Lack of Documentation

They are independent tools, despite being built off a common code base. So there is actually very

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Lack of Documentation

They are independent tools, despite being built off a common code base. So there is actually very

11/9/12

wlong...@systemsbiology.org

11/8/12

Getting Starting With BioFabric: Importing a .sif File

As a general rule, you will need to get started with BioFabric by importing a tab-delimited .sif file

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Getting Starting With BioFabric: Importing a .sif File

As a general rule, you will need to get started with BioFabric by importing a tab-delimited .sif file

11/8/12

wlong...@systemsbiology.org

10/29/12

Welcome to BioFabric Users!

This group is intended to answer questions, and to provide a forum for feedback and discussions,

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Welcome to BioFabric Users!

This group is intended to answer questions, and to provide a forum for feedback and discussions,

10/29/12

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