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Marko A. Rodriguez

Marko A. Rodriguez
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Connections in Time Some relationships change over time. Think about your friends from high school, college, work, the city you used to live in, the ones that liked you ex- better, etc. When exploring a social network it is important that we understand not only the strength of the relationship now, but over time. We can use communication between people as a measure. I ran into a visualization that explored how multiple parties where connected by communications in multiple projects. Let’s give our network a little something special. The code to create a relationship is pretty simple, we’ll use the Batch commands again and reference the nodes we create. Let’s put it together to create our graph. Our visualization was built using D3.js and it makes a web request expecting to see a JSON object that looks like: We spent some time getting our data into our graph, now let’s get it all back out. We’ll write another query to get the incoming relationships for each node. Like this: Like Loading...

bio4j blog | news and updates on bio4j Hello everyone, I’m happy to announce a new set of features for our tool Bio4jExplorer plus some changes in its design. I hope this may help both potential and current users to get a better understanding of Bio4j DB structure and contents. Node & Relationship properties You can now check with Bio4jExplorer the properties that has either a node or relationship in the table situated on the lower part of the interface. Name: property name Type: property type (String, int, float, String[], …) Indexed: either the property is indexed or not (yes/no) Index name: name of the index associated to this property -if there’s any Index name: type of the index associated to this property -if there’s any Node & Relationship Data source You can also see now from which source a Node or Relationship was imported, some examples would be Uniprot, Uniref, GO, RefSeq… Relationships Name property Get proteins (accession and names) associated to an interpro motif (limited to 10 results) I wish you all a great weekend!

Deploying the Aurelius Graph Cluster The Aurelius Graph Cluster is a cluster of interoperable graph technologies that can be deployed on a multi-machine compute cluster. This post demonstrates how to set up the cluster on Amazon EC2 (a popular cloud service provider) with the following graph technologies: Titan is an Apache2-licensed distributed graph database that leverages existing persistence technologies such as Apache HBase and Cassandra. Titan implements the Blueprints graph API and therefore supports the Gremlin graph traversal/query language. [OLTP] Faunus is an Apache2-licensed batch analytics, graph computing framework based on Apache Hadoop. Please note the date of this publication. Cluster Configuration The examples in this post assume the reader has access to an Amazon EC2 account. 1.~$ ssh ubuntu@ec2-184-72-209-80.compute-1.amazonaws.com 4.ubuntu@ip-10-117-55-34:~$ tar -xzf whirr-0.8.0.tar.gz Whirr is a cloud service agnostic tool that simplifies the creation and destruction of a compute cluster. 09. 10. 08. 09.

Corner Star Sorry for being tardy to the party. I'm not usually the one to make a fashionably late entrance, but this block boggled my mind for longer than usual. The Corner Star block is made up of flying geese and square in a square units. This tutorial lists measurements for a 16" block, since that's what we'll need for our project this week. Fabric Requirements: Fabric A (patterned or solid)Fabric B (patterned or solid, but different from A)Fabric C (for background) Step 1 - Cut fabric as follows Fabric A: Cut 16 2.5" squares (8" block -- 1.5")(12" block -- 2") Fabric B: Cut 16 2.5" squares (8" block -- 1.5")(12" block -- 2") Fabric C: Cut 9 4.5" squares (8" block -- 2.5")(12" block -- 3.5")Cut 4 2.5" squares (8" block -- 1.5")(12" block -- 2")Cut 12 2.5" x 4.5" rectangles (8" block -- 1.5" x 2.5")(12" block -- 2" x 3.5") Step 2 - Mark a diagonal line across the back of all Fabric A and Fabric B 2.5" squares. Step 3 - Trim seam allowance to 1/4" and press seams as desired. Step 4 - Repeat step two.

HyperGraphDB - A Graph Database HyperGraphDB is a general purpose, extensible, portable, distributed, embeddable, open-source data storage mechanism. It is a graph database designed specifically for artificial intelligence and semantic web projects, it can also be used as an embedded object-oriented database for projects of all sizes. The system is reliable and in production use is several projects, including a search engine and our own Seco scripting IDE where most of the runtime environment is automatically saved as a hypergraph. HyperGraphDB is primarily what its carefully chosen name implies: a database for storing hypergraphs. While it falls into the general family of graph databases, it is hard to categorize HyperGraphDB as yet another database because much of its design evolves around providing the means to manage structure-rich information with arbitrary layers of complexity. Key Facts Possible Usage Scenarios Semantic Web projects are an obvious domain of application of HyperGraphDB.

Neo4j Blog Suggesions on large scale web applications architecture Marmalade Squares (Two!) Quilt Author's Note: Thanks to readers who found errors in the tutorial. They have been fixed on the website but not pdf download. I will post here when the download has been fixed. A note from Oda May: Marmalade Squares is a popular name! Marmalade Squares is charm pack friendly and fun to sew—it would be a great baby gift or a charity quilt (just wrapped up 100 Quilts for Kids 2013 on my blog-- maybe you will join us next year?) 2 Charm Packs 1 ½ yards neutral Moda Bella Sand or other neutral solid (9900 201)2 ½ yards backing fabric 1 ¼ yards batting (or 44’’ x 50’’ piece of batting) 3/8 yard Stripe in Raspberry for binding (55054 12) Note: You may be able to use 1 charm pack + a little bit of coordinating fabric from the backing or your stash if you would like--the extra charms also work great as a stripe on the quilt back. 1. 2. 3. 4. 5. 6. 7. Cut some charm halves into 2.5’’ x 4.5’’ rectangles, and discard the remaining .5’’ x 2.5’’ rectangle. 8. 9. Putting Together the Quilt Top 1. 2.

phpCallGraph - A Static Call Graph Generator for PHP Disaster Area - Filed under 'neo4j' I recently helped add versioning support to Neo4j.rb . Versioning only works for Rails models at the moment. To add versioning to your model, you'll need include the Versioning module: How it works Versioning creates snapshots under a given rails model instance. Note that snapshots aren't Rails models, but vanilla nodes. Full snapshots Snapshots currently capture all the properties of an instance. Let's look at an example: With version 1 of the driver, there are no links to any cars: With version 2, we link the driver to a sports car - a Porsche. Now, both the driver and the current version are linked to the Porsche. With version 3, we link the driver to a second car - a Ferrari. The driver, as well as the latest snapshot, are both linked to two cars - the Porsche and the Ferrarri. Working with a version To retrieve a snapshot, you'll need to call the version API. The snapshot object will respond to the exact same properties as those on instance. Reverting to a snapshot Max versions Gotchas

3.4 Scaling Web Applications We have regarded the scalability of web applications from an architectural point of view so far. In the next chapters, we will focus on scalability within web architectures, based on the usage of concurrency inside web servers, application servers and backend storage systems. However, there are other factors which influence the scalability and perceived performance of web applications. Therefore, we will provide a brief overview of factors relevant for web site setup and client-side web application design. The overview summarizes important strategies outlined in relevant books[All10,Abb11,Abb09] and a blog article from the Yahoo Developer Network. From a user's perspective, a web applications appears scalable, when it continues to provide the same service and the same quality of service independent of the number of concurrent users and load. Optimizing Communication and Content Delivery First and foremost, it is very important to minimize the number of HTTP requests.

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