SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction.

We present the jump-start simultaneous alignment and tree construction using hidden Markov models (SATCHMO-JS) web server for simultaneous estimation of protein multiple sequence alignments (MSAs) and phylogenetic trees. The server takes as input a set of sequences in FASTA format, and outputs a phylogenetic tree and MSA; these can be viewed online or downloaded from the website. SATCHMO-JS is an extension of the SATCHMO algorithm, and employs a divide-and-conquer strategy to jump-start SATCHMO at a higher point in the phylogenetic tree, reducing the computational complexity of the progressive all-versus-all HMM-HMM scoring and alignment. Results on a benchmark dataset of 983 structurally aligned pairs from the PREFAB benchmark dataset show that SATCHMO-JS provides a statistically significant improvement in alignment accuracy over MUSCLE, Multiple Alignment using Fast Fourier Transform (MAFFT), ClustalW and the original SATCHMO algorithm. The SATCHMO-JS webserver is available at http://phylogenomics.berkeley.edu/satchmo-js. The datasets used in these experiments are available for download at http://phylogenomics.berkeley.edu/satchmo-js/supplementary/

cyTRON and cyTRON/JS: two Cytoscape-based applications for the inference of cancer evolution models

The increasing availability of sequencing data of cancer samples is fueling the development of algorithmic strategies to investigate tumor heterogeneity and infer reliable models of cancer evolution. We here build up on previous works on cancer progression inference from genomic alteration data, to deliver two distinct Cytoscape-based applications, which allow to produce, visualize and manipulate cancer evolution models, also by interacting with public genomic and proteomics databases. In particular, we here introduce cyTRON, a stand-alone Cytoscape app, and cyTRON/JS, a web application which employs the functionalities of Cytoscape/JS. cyTRON was developed in Java; the code is available at https://github.com/BIMIB-DISCo/cyTRON and on the Cytoscape App Store http://apps.cytoscape.org/apps/cytron. cyTRON/JS was developed in JavaScript and R; the source code of the tool is available at https://github.com/BIMIB-DISCo/cyTRON-js and the tool is accessible from https://bimib.disco.unimib.it/cytronjs/welcome

Interactive Geometric Algorithm Visualization in a Browser

We present an online, interactive tool for writing and presenting interactive geometry demos suitable for classroom demonstrations. Code for the demonstrations is written in JavaScript using p5.js, a JavaScript library based on Processing

Node JS Performance Testing

Node JS, a server side implementation of JavaScript, has gained traction over the years, especially in newer tech startups, to be used in deployment servers. Performance testing is a set of tests intended to measure the speed and reliability of a server under various loads . This project examines performance testing applied to Node JS, design decisions of the testing environment, and quantitative analysis of server improvements made to increase performance of the server of Music Putty, a music streaming and crowdfunding startup formed at Cal Poly

Syndrome X

JS, a 34-year-old contractor, presented with a two day history of a sore throat. He was noted to have become increasingly centrally obese since his last visit – which he blamed on having gotten married in the interim – and was known to be a smoker. JS’ sore throat was his priority. However, a family history of diabetes mellitus and his history of ‘borderline’ hypertension were of more concern to his doctor. Is this the metabolic syndrome? How should this patient be managed? With a name as elusive as Syndrome X, it is all too easy to dismiss the topic as a rather exotic phenomenon for the internists and researchers to deal with. Nevertheless, what was described as Syndrome X in 1988 by Gerald Reaven and is now referred to as metabolic syndrome, appears to be one of the commonest conditions encountered in general practice. The metabolic syndrome, being a syndrome should innately be a collection of signs and symptoms of a pathological process together constituting a picture of a particular clinical condition warranting particular management. The gist of it all can be seen to lie in different perspectives; the metabolic syndrome can be seen as: • ‘simply’ a clustering of cardiovascular risk factors – possibly preventable and treatable or, • a multiplex of metabolic risk conditions namely atherogenic dyslipidaemia, hypertension, glucose intolerance, a proinflammatory and a prothrombotic state. This offers, perhaps, a more pathophysiological description of the condition. When it comes to the young gentleman described above, dismissing his possible collection of risk factors or failing to give them their due importance can result in the loss of a precious opportunity at preventive care which is definitely neither exotic nor beyond the scope of the primary care physician.peer-reviewe

Financial asset bubbles in banking networks

We consider a banking network represented by a system of stochastic differential equations coupled by their drift. We assume a core-periphery structure, and that the banks in the core hold a bubbly asset. The banks in the periphery have not direct access to the bubble, but can take initially advantage from its increase by investing on the banks in the core. Investments are modeled by the weight of the links, which is a function of the robustness of the banks. In this way, a preferential attachment mechanism towards the core takes place during the growth of the bubble. We then investigate how the bubble distort the shape of the network, both for finite and infinitely large systems, assuming a non vanishing impact of the core on the periphery. Due to the influence of the bubble, the banks are no longer independent, and the law of large numbers cannot be directly applied at the limit. This results in a term in the drift of the diffusions which does not average out, and that increases systemic risk at the moment of the burst. We test this feature of the model by numerical simulations.Comment: 33 pages, 6 table

The geography of industrial plant ŠKODA JS a. s.

Předložená bakalářská práce je zaměřena na charakteristiku průmyslového závodu situovaného v okrese Plzeň-město, konkrétně závod ŠKODA JS a.s. V první části práce jsou stanovené cíle práce a dále rozbor vhodné odborné literatury, která byla využita. Druhá část popisuje vybraný region, ve kterém je závod lokalizován. Tato část obsahuje charakteristiku z geografického hlediska. Třetí část charakterizuje vybraný závod, jeho historii, účast ve společnostech, hlavní činnosti a organizační strukturu. Čtvrtá část je zaměřena na analýzu pracovníků závodu, jejich vývoj, strukturu a dojížďku do závodu a také se zabývá personální a mzdovou politikou, která se v závodě uplatňuje. Pátá část blíže specifikuje dodavatelsko-odběratelské vztahy, díky kterým závod proniká na trh. Poslední část práce řeší pozitivní i negativní vlivy závodu na region.ObhájenoPresented bachelor thesis is focused on the characteristics of the industrial plant situated in the district Pilsen-town, namely ŠKODA JS a.s. In the first part of this thesis are set goals of work and analysis of appropriate professional literature, which was used. The second part describes the selected region in where the plant is located. This section contains a geographic aspect. The third part is describing the chosen factory, its history, participation in companies, main activities and organizational structure. The fourth part is focused on the analysis of factory staff, their development, structure and commuting, and also deals with the personnel and wage policy which applied. The fifth part specifies the supplier-customer relationship, which makes the plant penetrate the market. The last part of this thesis deals with the positive and negative effects on the region

Hysteresis in a bimetallic holmium complex : A synergy between electronic and nuclear magnetic interactions

We report a bimetallic holmium(III) complex showing a S-shaped magnetic hysteresis at low temperature. The complex is investigated by x-ray crystallography, magnetometry, single crystal microsquid measurements, and first-principles calculations. A model Hamiltonian including electronic and nuclear magnetic moments is used to fit all experimental data. We conclude that the Ho(III) may be described as non-Kramers doublets with respective gaps of Delta(A) = 0.8 and Delta(B) = 10 cm(-1) and that there is a small ferromagnetic coupling of J = 1 cm(-1) ((H) over cap (S) = -JS(A) . S-B). As in previous works, the hysteresis arise from the hyperfine structure of the Ho(III) ions. The S-shaped form of the hysteresis reflects the avoided crossing of the electronic states in the non-Kramers doublets.Peer reviewe