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1.
The plug-in concept
Peter Šenk, 2013, review article

Abstract: The architecture concept of plug-in is based on the duality of the infrastructure system and units or elements connected to it. In the context of megastructures, the concept was most vividly characterised by works of Archigram and Japanese Metabolists in the 1960s and early 1970s. Blurring the boundary between the building and the city, the plug-in concept outgrew architectural boundaries and was slowly transformed into an urbanistic concept. The paper presents the cultural context relevant to contemporaneity, which influenced specific development of the technology-driven concept of plug-in in the British Archigram Group and Japanese Metabolists. Based on the aesthetics of change and incompleteness, which was characterised by similar architectural manifestations despite entirely different cultural backgrounds, the plug-in concept foreshadowed social transformation based on freedom, individualisation and mobility in an utopian manner and held a promise of urban development with adaptability to unpredictable needs and desires of residents, who would become its co-creators with an active approach. Although the revolutionary sixties are quite some time behind, the plug-in concept in its commodified form has become and remained operational and relevant at least on the metaphorical level; in the contemporary space it is evident primarily in urbanism and not as much in its original architectural form.
Keywords: plug-in, clip-on, Reyner Banham, Archigram, Metabolism
Published: 21.12.2015; Views: 620; Downloads: 45
.pdf Full text (1,66 MB)
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2.
Iskanje vezavnih mest in rangiranje genov na podlagi CLIP in RNAseq podatkov
Nejc Haberman, 2013, master's thesis

Abstract: Proteini, ki se vežejo na RNK (ang. RNA-binding proteins), imajo pomembno vlogo pri regulaciji posttrankripcijskih procesov in so ključni regulatorji genske ekspresije. Za preučevanje vezavnih proteinov na RNK v živih celicah sta najprimernejši metodi CLIP (UV cross-linking and immunoprecipitation) in iCLIP (individual-nucleotide resolution CLIP). RNA-seq je postala standardizirana metoda za merjenje genske ekspresije celotnega transkriptoma. V naši raziskavi smo preučevali najprimernejšo normalizacijo CLIP-podatkov z RNA-seq podatki. Glavni problem je, da posamezna CLIP/iCLIP-metoda določi več vezavnih mest v visoko izraženih delih molekule RNK, ki posledično prekrijejo nizko izražena vezavna mesta. Zato je potreba po RNA-seq podatkih, da lahko z njimi normaliziramo vezavna mesta CLIP/iCLIP- podatkov. V ta namen smo načrtovali in implementirali različne metode normalizacij CLIP- in RNA-seq podatkov in jih primerjali z do sedaj znanimi rezultati za protein LIN28A. V našo raziskavo smo vključili programsko orodje Piranha, ki že uporablja metodo normalizacije z regresijskim modelom ZTNBR (zero-truncated negative binomial distributions regression), ki pa se ni izkazala za primerno rešitev našega problema. Izdelali smo hibridno metodo, ki izboljša objavljeno metodo, ki uporablja preprosto normalizacijo vsote RNA-seq odčitkov pri proteinu LIN28A. Hibridna metoda uporablja statistični model ZTNB (zero-truncated negative binomial distributions) za identifikacijo signifikantnih vezavnih mest in je del programskega orodja Piranha. Za vse opisane metode normalizacij smo razvili cevovod programskih skript in bioinformatskih orodij za primerjalno analizo metod. Prav tako smo razvili programski cevovod za preprocesiranje iCLIP-podatkov, ki jih lahko uporabimo v omenjenih normalizacijah. Vse metode bodo prosto dostopne na spletu in se bodo lahko uporabljale v prihodnjih raziskavah za analizo vezavnih proteinov na RNK s CLIP/iCLIP- in ostalimi sorodnimi metodami sekveniranja.
Keywords: normalizacija, vezavni proteini na RNK, CLIP, iCLIP, RNA-seq, LIN28A, bioinformatska orodja, genska obogatitev
Published: 06.08.2013; Views: 1533; Downloads: 161
.pdf Full text (2,11 MB)

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