22 free tools for data visualization and analysis You may not think you've got much in common with an investigative journalist or an academic medical researcher. But if you're trying to extract useful information from an ever-increasing inflow of data, you'll likely find visualization useful -- whether it's to show patterns or trends with graphics instead of mountains of text, or to try to explain complex issues to a nontechnical audience. There are many tools around to help turn data into graphics, but they can carry hefty price tags. The cost can make sense for professionals whose primary job is to find meaning in mountains of information, but you might not be able to justify such an expense if you or your users only need a graphics application from time to time, or if your budget for new tools is somewhat limited. If one of the higher-priced options is out of your reach, there are a surprising number of highly robust tools for data visualization and analysis that are available at no charge. Data cleaning DataWrangler
Data | 1000 Genomes Sample lists and sequencing progress A summary of sequencing done for each of the three pilot projects is available here. The list of samples and allocations is provided in a spreadsheet. Variant Calls Our variant calls are always released in vcf format. Alignments The main project alignments are available in BAM format. Raw sequence files The main project raw sequence data is available in fastq format. Download data The sequence and alignment data generated by the 1000genomes project is made available as quickly as possible via our mirrored ftp sites. EBI FTP: NCBI FTP: Users in the Americas should use the NCBI ftp site and users in Europe and the rest of the world should use the EBI ftp site The data is also available via an Aspera server from both sites. The plugin should automatically start when you visit either the EBI Aspera site or the NCBI Aspera site. An example command line for ascp looks like:
Software: Is 'Social' Business Collaboration Just an Expensive Fad? I'm not sure that social networking technology -- particularly in the form that vendors are currently presenting it -- offers the best approach for improving business collaboration. Many of these vendors are asking corporations to make significant investments in applications that do little more than mimic Facebook. Webinar: The New PCI 3.0 Standard Learn the steps to take to get your company ready for PCI DSS 3.0 changes coming January 2015. Social networking technology has found a solid niche in the business world. Major corporations like Pepsi and Procter & Gamble have been so happy with the results of their various social media campaigns that they have shifted large portions of their advertising budgets from more traditional channels like print and television to the social networking realm. These trends also have grabbed the attention of business applications developers. Enhancing Business Collaboration How Is This Different? This Isn't Social Networking
User Page - sbgn.org SBGN study guide Visit the Documents section for: various examples (to get a better idea of what an actual map looks like) some tutorials (very accessible, but not always up-to-date) publications about SBGN (a good start for a brief historical overview) detailed technical specifications (the ultimate reference documents, most up-to-date, but a steep learning curve for beginners) some Frequently Asked Questions Please also check the SBGN PD User Manual when you are ready to draw your own maps. Quick overview The Systems Biology Graphical Notation comprises three complementary languages suited to represent different types of pathways. Process Descriptions (PD) is a language that permits the description of the processes (e.g. biochemical reactions) taking place in a biological system. Entity Relationships (ER) is a language that permits the description of all the relations involving the entities of a biological system. Language reference cards SBGN Bricks dictionary Getting started User Manual
Information retrieval Information retrieval is the activity of obtaining information resources relevant to an information need from a collection of information resources. Searches can be based on metadata or on full-text (or other content-based) indexing. Automated information retrieval systems are used to reduce what has been called "information overload". Many universities and public libraries use IR systems to provide access to books, journals and other documents. Web search engines are the most visible IR applications. Overview[edit] An information retrieval process begins when a user enters a query into the system. An object is an entity that is represented by information in a database. Most IR systems compute a numeric score on how well each object in the database matches the query, and rank the objects according to this value. History[edit] Model types[edit] For effectively retrieving relevant documents by IR strategies, the documents are typically transformed into a suitable representation. Recall[edit]
UMLS Terminology Services -- Home The 9 kinds of context that will define contextual search Yesterday I did the kick-off presentation and workshop at a strategy planning session of a major online media company. The intent was to provide some different perspectives on trends in digital media as input to their deliberations. One of the many topics I discussed was the rise of contextual search. Looking back over the last decade, I think it’s fair to say that the search experience has not evolved much. Clearly it is a nonsense to always get the same search result, irrespective of who you are and all of the conditions surrounding the search. At LeWeb ’10 Marissa Mayer of Google described “contextual discovery”: “The idea is to push information to people,” Mayer said. Here are 8 kinds of context that could be taken into account by information discovery engines (if the context is available). * Individual. * Demographic profile. * Interest profile. * Location. * Device. * Date. * Time. * Weather. * Mood. (Please add any thoughts on other relevant context in comments.) Push. Behaviors.
CCSB Interactome Database Preliminary Human Binary Interactome Datasets Available 1. 13,944 unpublished binary protein-protein interactions (HI-II-11)2. Human ORF collection for binary interaction screening here3. Binary protein-protein interactions from test search space here H uman interactome mapping is the flagship project of CCSB. Viruses intrinsically depend on their host cell during the course of infection and can elicit pathological phenotypes similar to those arising from mutations (Gulbahce et al PLoS Comput Biol 2012). Plants have unique features that evolved in response to environmental and ecological challenges. Yeast Interactome version 1 (CCSB-YI1) contains high-quality yeast two-hybrid protein-protein interactions for S. cerevisiae. Fragmentome: Many protein-protein interactions are mediated through independently folding modular domains.
Crowdsourcing and Crowdfunding News and Headlines American Biotechnologist Much-needed tool for neuroscience emerges after years of work :: Posted by American Biotechnologist on 04-24-2014 Nearly a decade ago, the era of optogenetics was ushered in with the development of channelrhodopsins, light-activated ion channels that can, with the flick of a switch, instantaneously turn on neurons in which they are genetically expressed. The new structurally engineered channel at last gives neuroscientists the tools to both activate and inactivate neurons in deep brain structures using dim pulses of externally projected light. First discovered in unicellular green algae in 2002, channelrhodopsins function as photoreceptors that guide the microorganisms’ movements in response to light. Read more… Advice from a Nobel Prize Laureate :: Posted by American Biotechnologist on 04-23-2014 Want to become a Nobel Prize winner? Don’t listen to anybodyDon’t think about “Big” ideasYour supervisor is decrepit and old…forget about his advice!
The Grand Collaboration Convergence The Collaboration Chaos In recent times, solutions of all kinds have been launched and marketed under the "online collaboration software" banner. At first look, there seems to be not much in common in these different solutions, even though the propose to solve the same business need. Indeed, they also fit the dictionary meaning of online collaboration - the ability to work together on information across locations. But how is a consumer to navigate through this vast array of solutions, and how is an analyst to conceptualize them? Different Approaches to Collaboration The areas of approach can be identified as follows - document management, intranet (workspaces), messaging (email, contacts, calendars), wiki, project management, social networking, microblogging, and web conferencing. A Grand Convergence? These solutions do not represent non intersecting sets. Infact, in recent times, the market is seeing a convergence of sorts. Would you like to see your solution on the graph?