Author Archives: Marco Barnig

DLNA : Digital Living Network Alliance

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Last update : June 17, 2012;

DLNA logo

The Digital Living Network Alliance (DLNA) allows consumers to connect and enjoy their music, videos and photos from any consumer device (computers, printers, cameras, cell phones, and other multimedia devices) from anywhere in their homes. DLNA (website : dlna.org) is a non-profit collaborative trade organization established by Sony in June 2003, that is responsible for defining interoperability guidelines to enable sharing of digital media between these devices . The private guidelines are built upon existing public standards and specify a set of restricted ways of using the standards in order to achieve interoperability.

Today there are 26 promoter members and 199 contributor members. In early 2011, DLNA began a Software Certification program in order to make it easier for consumers to share their digital media across a broader range of products. Today there are over nine thousand products on the market that are DLNA certified.

DLNA uses Universal Plug and Play (UPnP) for media management, discovery and control.

The DLNA Certified Device Classes are separated as follows :

  • Digital Media Servers (DMS) store content and make it available to networked media devices
  • Digital Media Controller (DMC) find content on digital media servers and play it on digital media renderers
  • Digital media renderers (DMR) play content received from a digital media controller
  • Digital media players (DMP) find content on the network and provide playback and rendering capabilities
  • Digital media printers (DMPr) provide printing services to the DLNA home network

Examples for DMS include personal computers or network-attached storage (NAS) devices. All DLNA devices can be mobile (wireless). Bridges between mobile handheld device network connectivity and home network connectivity are provided by  Mobile Network Connectivity Functions (M-NCF). Content transformations between required media formats for home network and mobile handheld devices iare provided by Media Interoperability Units (MIU).

DLNA is a refinement of UPnP, a set of rules and restrictions in the name of interoperability. Full DLNA specifications are available only to DLNA members who pay for. UPnP specifies the abstract device interfaces, the specifications for UPnP are available at the UPnP forum.

RESS: Responsive Design + Server Side Components

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Last update : June 26, 2014

In Responsive Web Design implementations, Web URLs are consistent across devices and adapt their content based on the capabilities of the browser in which they are displayed.

Server side solutions, on the other hand, only send what a client needs. But server-side solutions generally rely on user agent redirects to device-specific code templates. Each device class that warrants adaptation needs its own set of templates and these templates may ultimately contain duplicative code that actually applies to every class of device.

JavaScriptObject

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JavaScriptObject is an application to publish 3D models in a userfriendly way. The principle is simple: A 3D model is rotated by a given step width around two axes. An image of the model is rendered at each step. After a full revolution around both axes one has a “complete” frameset of the object. Finally the JavaScript shows a single frame out of the image pool in relation to the mouse position and thereby creates the illusion of an 3D object.

JavaScriptObject was developed by Finn Rudolph from Germany. The current version is 0.9.3 released in 2009.

 

Google Art Project

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The Google Art Project is a unique online art experience, using a combination of various advanced Google technologies and expert information, provided by 151 acclaimed art partners (museums, galleries, …) from across 40 countries.

Google Art Project

Users can

  • explore a wide range of artworks at brushstroke level detail
  •  take a virtual tour of a museum or gallery (with Street View images and navigation)
  • build their own collections to share (user gallery)
  • enjoy over 30 000 artworks from sculpture to architecture
  • explore over 150 collections
  • edit, reorder, upload Youtube videos and more in the “My Galleries” section
  • use a dedicated Education section providing simple tools to learn about the artworks featured on the Google Art Project

The Google Art Project was launched on 1 February 2011. Seventeen galleries and museums were included in the launch of the project.

In France, the Centre de recherche et de restauration des musées de France (C2rmf) launched in 2009 the project 3D*COFORM to advance the state-of-the-art in 3D-digitisation and make 3D-documentation an everyday practical choice for digital documentation campaigns in the cultural heritage sector.

WordPress Post Formats

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Post formats have been around since WordPress 3.1. They specify the format applied to a content. Post formats are different from Post Types which specify the type of content : post, page or maybe a custom type like books or products.

The following Post Formats are supported :

  • standard : post with title, date and author
  • aside : post without title and data, with the hint “aside”
  • link : post without title and data, with the hint “link”
  • gallery : first picture of a native gallery and number of pictures in the gallery
  • status : format like Twitter, with a gravatar
  • quote : post without title and data, with the hint “quote”
  • image : special format for photoblogging
  • video : special format for videos
  • audio : special format for audios
  • chat : special format for chat logs

Post Formats

The WordPress theme Twenty Ten supports the standard, aside and gallery format. The new theme Twenty Eleven supports all formats, but video, audio and chat need to be activated by adding them to the post formats array in the theme file functions php :

// Add support for a variety of post formats
add_theme_support( 'post-formats', array( 'aside', 'link', 'gallery', 'status', 'quote', 'image', 'chat', 'video', 'audio' ) );

They need to be styled further in the corresponding css-file.

To add the Post Formats in a child theme, you must ensure that the childtheme setup occurs after the parenttheme setup. This is the code :

function childtheme_setup(){ add_theme_support( 'post-formats', array( 'aside', 'link', 'gallery', 'status', 'quote', 'image', 'chat', 'video', 'audio' ) ); add_action( 'after_setup_theme', 'childtheme_setup' );

The following list shows links to useful tutorials and documentation about WordPress Post Formats :

Hereafter are some older posts about WordPress themes and templates :

LA Re.Play : an exhibition of mobile media art

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LA Re.Play, an exhibition of Mobile Art, took place in Los Angeles, February 22-29, 2012. 

Playing upon the dynamic relations between physical place, digital space, and mobile access via smartphone, the mobile artworks highlighted in the exhibit and the panels adopt elements of location-based performance, mobile gaming, and mobile, networked activism to highlight the embodied performance of hybrid place and the social and collective politics of networked space. LA Re.Play explored art that incorporates cell phones, GPS and other mobile technology, revealing the complex social, political, technological and physiological effects of new mixed reality interactions.

LA.Replay was curated by Hana Iverson, Mimi Sheller and Jeremy Hight.

Central dogma of molecular biology

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Last update : August 9, 2013

The central dogma of molecular biology is not really a dogma, but a framework for understanding the transfer of sequenced information between biopolymers in living organisms. There are 3 major classes of such biopolymers :

  • DNA
  • RNA
  • Protein

In it’s simplest form, the dogma of molecular biology states that DNA makes RNA and RNA makes protein. The dogma was first stated by Francis Crick in 1958 and re-stated in a Nature paper (Vol 227) published in August 1970.

There are 3×3 = 9 conceivable direct transfers of information that can occur between these biopolymers classed into 3 groups :

  • general transfers
  • special transfers
  • unknown transfers

The general transfers describe the normal flow of biological information :

  • DNA Replication : process by which one double-stranded DNA molecule produces two identical copies of the molecule
  • Transcription : process by which the information contained in a section of DNA is transferred to a newly assembled piece of messenger RNA (mRNA)
  • Translation : process by which the messenger RNA (mRNA) produced by transcription is decoded by the sites of protein synthesis, the ribosomes, to produce a specific amino acid chain, or polypeptide, that will later fold into an active protein

Special transfers occur only under specific conditions in case of some viruses or in a laboratory. These transfers are RNA replication, reverse transcription and direct translation from DNA to protein.

Francis Crick believed that protein could not encode for DNA or RNA or other proteins and classed these processes in the unknown transfers. Prions, discovered in 1982 by Stanley B. Prusiner, are proteins that propagate themselves by making conformational changes in other molecules of the same type of protein. While this represents a transfer of information from protein to protein, prion interactions leave the sequence of the protein unchanged, and so are not technically considered an exception to the central dogma of molecular biology of Francis Crick.

GeneChip Expression Analysis Technology

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DNA oligonucletides (oligo) are short stretches of DNA sequences. Due to the double-stranded nature of DNA, one can design an oligo which has the complementary sequence to any gene of interest. If these oligos, or probes, are attached to a solid surface in a defined grid (x rows and y columns), a genechip (also called microarray or DNA chip) has been created.

If the genechip is put in contact with a solution containing sequences of gene products, these products (targets) will bound with their complementary probes. This process is called hybridization. The more products of a gene are in the solution, the more will hybridize with the probe on the surface of the microarray.

To identify the hybridized targets, it is necessary to label them. There are several techniques to do this marking. Beneath labeling with radioactive isotopes, the most common non-radioactive technique is fluorescent dye (FISH : fluorescence in situ hybridization). Most popular are Cyanine dyes, especially Cy3, fluorescent in the green region and Cy5, fluorescent in the red region.

One dye color is sufficient to measure the abundance of particular gene products in particular regions by scanning the microarray. The most common approach however is a two-color design where one of the samples of the gene products is a universal reference sample.

A gene product is the biochemical material, either functional RNA or protein, resulting from the activity (expression) of a gene. The amount of gene products depends on how active a gene is. In most experiments the ribosomal RNA (rRNA) is used as the gene product, because rRNA is one of only a few gene products present in all cells. Ribosomal RNA provides a mechanism for decoding mRNA into amino acids.

After the hybridization, the unbound material is washed away and the microarray is scanned. Once the data is collected, it can be analyzed by sophisticated bioinformatics tools. The results are usually published and shared with the scientific community in specialized data-bases.

The following list of links provides further informations and some interactive animations about genechip expression analysis technologies :

Fold change in analysis of gene expression

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Fold change is often used in analysis of gene expression data in microarray and RNA-Seq experiments, for measuring change in the expression level of a gene.

Fold change is a number describing how much a quantity changes going from an initial to a final value. For example, an initial value of 30 and a final value of 60 corresponds to a fold change of 2 (in common terms, a two-fold increase). A change from 80 to 20 would be a fold change of 0.25, while some practitioners replace a fold-change value that is less than 1 by the negative of its inverse, e.g.0.25 would be a fold change of -4 (in common terms, a four-fold decrease).

Agilent Sureprint G3 Human Gene Expression 8x60K Microarray

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Agilent’s SurePrint G3 Human GE 8x60K Microarray is based on updated transcriptome databases for mRNA targets and also include probes for lincRNAs (long intergenic non-coding RNAs). With the combination of mRNA and lincRNAs, it is now possible to perform two experiments on a single microarray, confidently predicting lincRNA function.

Each kit contains 3 standard glass slides containing eight 60K 60-mer Oligonucleotide microarray printed using Agilent’s SurePrint technology. The product number is G4851A, the design ID is 028004.

Each array contains 62,976 features arranged in 384 rows and 164 columns. A GeneList of the spots contained in the 8X60K microarrays is available at the Agilent Technologies website. There are 40.509 different genes, several are duplicated.

The following list shows the typical tools to analyze the Agilent microarrays :