Author Archives: Marco Barnig

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 :

Gene Expression Omnibus (GEO) and MIAME

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GEO is a public repository that archives and freely distributes microarray, next-generation sequencing, and other forms of high-throughput functional genomic data submitted by the scientific community. In addition to data storage, a collection of web-based interfaces and applications are available to help users query and download the studies and gene expression patterns stored in GEO. Submitters are encouraged to supply MIAME compliant data.

The MIAME (Minimum Information About a Microarray Experiment) guidelines outline the minimum information that should be included when describing a microarray experiment. The six most critical elements contributing towards MIAME are :

  • raw data for each hybridization
  • final processed (normalized) data for the set of hybridizations in the experiment
  • essential sample annotation including experimental factors and their values
  • experimental design including sample data relationships
  • sufficient annotation of the array
  • essential laboratory and data processing protocols

Many journals require accession numbers for microarray or sequence data before acceptance of a paper for publication. GEO processing times is approximately 5 business days after completion of submission.

GEO is hosetd by the NCBI (National Center for Biotechnology Information).  A detailed documentation is available at the NCBI website. Specific recommendations for Agilent submissions are also available.

Genome Assembly Terminology

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Below is a list of commonly used terms and definitions in the field of genomics (source : Genome Reference Consortium).

  • Assembly : a set of chromosomes, unlocalized and unplaced sequences and alternate loci used to represent an organism’s genome
  • Chromosome Assembly : a relatively complete pseudo-molecule assembled from smaller sequences that represent a biological chromosome
  • Diploid Assembly : a genome assembly for which a Chromosome Assembly is available for both sets of an individual’s chromosomes
  • Haploid Assembly : the collection of Chromosome assemblies, unlocalized and unlocalized sequences and alternate loci that represent an organism’s genome
  • Primary Assembly : a primary assemblies represents the collection of assembled chromosomes, unlocalized and unplaced sequences that, when combined, should represent a non-redundant haploid genome
  • Assembly Units : collections of sequences used to define discrete parts of an assembly
  • Genome Patch : a contig sequence that is released outside of the full assembly release cycle
  • FIX patch : FIX patches are released to correct an error in the assembly and will be removed when the new full assembly is released
  • NOVEL patch : NOVEL patches are sequences that were not in the last full assembly release and will be retained with the next full assembly release
  • Alternate Locus :
  • Unlocalized Sequence : a sequence found in an assembly that is associated with a specific chromosome but cannot be ordered or oriented on that chromosome
  • Unplaced Sequence : a sequence found in an assembly that is not associated with any chromosome
  • PAR (Pseudo-autosomal region) : a region found on the X and Y chromosomes of mammals that allow recombination between the sex chromosomes
  • AGP File : a file used to describe the instructions for building a contig, scaffold or chromosome sequence
  • Contig : a contiguous sequence generated from determining the non-redundant path along an order set of component sequences
  • Component : a low genomic level sequence used to construct the genome, typically these are either clone sequences, WGS sequence or a PCR fragment
  • Join : the sequence overlap between two adjacent components in a contig
  • Scaffold : an ordered and oriented set of contigs with gaps
  • Switch Point : the base at which the contig sequence stops being generated from one component sequence and switches to using the next component sequence
  • TPF (Tiling Path file) : provides the order of the component sequences used to build a contig, scaffold or chromosome