Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation.

The international Functional Annotation Of the Mammalian Genomes 4 (FANTOM4) research collaboration set out to better understand the transcriptional network that regulates macrophage differentiation and to uncover novel components of the transcriptome employing a series of high-throughput experiments. The primary and unique technique is cap analysis of gene expression (CAGE), sequencing mRNA 5'-ends with a second-generation sequencer to quantify promoter activities even in the absence of gene annotation. Additional genome-wide experiments complement the setup including short RNA sequencing, microarray gene expression profiling on large-scale perturbation experiments and ChIP-chip for epigenetic marks and transcription factors. All the experiments are performed in a differentiation time course of the THP-1 human leukemic cell line. Furthermore, we performed a large-scale mammalian two-hybrid (M2H) assay between transcription factors and monitored their expression profile across human and mouse tissues with qRT-PCR to address combinatorial effects of regulation by transcription factors. These interdependent data have been analyzed individually and in combination with each other and are published in related but distinct papers. We provide all data together with systematic annotation in an integrated view as resource for the scientific community (http://fantom.gsc.riken.jp/4/). Additionally, we assembled a rich set of derived analysis results including published predicted and validated regulatory interactions. Here we introduce the resource and its update after the initial release.

From Caregiver to Computer Geek: The Design of a Web Resource for Novice Clinical Informaticians

Introduction: Throughout the United States, there are massive initiatives in place to reform healthcare through the implementation of electronic health records. The goals are to improve patient care through improved access to records, the improvement of business and reimbursement processes, streamlining of clinician workflows for increased efficiency, and reducing the variability in the delivery of patient care. [See PDF for complete abstract]

ViralZone: a knowledge resource to understand virus diversity.

The molecular diversity of viruses complicates the interpretation of viral genomic and proteomic data. To make sense of viral gene functions, investigators must be familiar with the virus host range, replication cycle and virion structure. Our aim is to provide a comprehensive resource bridging together textbook knowledge with genomic and proteomic sequences. ViralZone web resource (www.expasy.org/viralzone/) provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures.

TU Graz: Course: 707.000 Web Science and Web Technology: Lecture 11: User Intentions and Intentional Structures on the Web

Search engines - such as Google - have been characterized as "Databases of intentions". This class will focus on different aspects of intentionality on the web, including goal mining, goal modeling and goal-oriented search. Readings: M. Strohmaier, M. Lux, M. Granitzer, P. Scheir, S. Liaskos, E. Yu, How Do Users Express Goals on the Web? - An Exploration of Intentional Structures in Web Search, We Know'07 International Workshop on Collaborative Knowledge Management for Web Information Systems in conjunction with WISE'07, Nancy, France, 2007. [Web link] Readings: Automatic identification of user goals in web search, U. Lee and Z. Liu and J. Cho WWW '05: Proceedings of the 14th International World Wide Web Conference 391--400 (2005) [Web link]

TU Graz: Course: 707.000 Web Science and Web Technology: Lecture 13: Web Technologies 2 - The Semantic Web

The semantic web represents a current research effort to increase the capability of machines to make sense of content on the web. In this class, Peter Scheir will give a guest lecture on the basic principles underlying the semantic web vision, including RDF, OWL and other standards.

Individuals, Behaviour Change and the Web

A psychologist's description of the Web as an effective channel for inducing and promoting changes of behaviour in individuals. Demonstrates an experimental system called "LifeGuide".

The Sociology of the Web

A sociologist's description of the Web as a socially constructed/discovered/encountered piece of technology.

Law, The Universe and Everything. The Regulation of the Web

Web Science lecture about the impact of law on the web and vice versa.

Who Invented the Web?

It is received wisdom that Tim Berners-Lee invented the Web; but there is a lot more technology and historical context that plays a part.

Communities and the Web

What is a social network? How does an online community differ from a real world community? See also: Anne Hornsby, 'Surfing the net for community: a Durkheimian analysis of electronic gatherings' ch.3 in Peter Kivisto (ed.) Illuminating Social Life (3rd ed 2005). Libr ref HM51KIV. Graham Crow and Catherine Maclean, 'Community' in Geoff Payne (ed.) Social Divisions (2nd ed. 2006) HM821PAY.

Mapping the Web

Different attempts to 'map' different aspects of the web. How do you impose some sort of high level understanding onto the Web Graph?

Using EndNote Web

This is a handout to describe how to use EndNote Web v2.7. It is focused on the BioMedical area and covers linking to PubMed, Web of Knowledge, other bibliographic providers (OVID and EBSCO) and searching for book information. The notes include how to use Word 2003 and Word 2007