High-Performance Cloud Computing: A View of Scientific Applications

Scientific computing often requires the availability of a massive number of computers for performing large scale experiments. Traditionally, these needs have been addressed by using high-performance computing solutions and installed facilities such as clusters and super computers, which are difficult to setup, maintain, and operate. Cloud computing provides scientists with a completely new model of utilizing the computing infrastructure. Compute resources, storage resources, as well as applications, can be dynamically provisioned (and integrated within the existing infrastructure) on a pay per use basis. These resources can be released when they are no more needed. Such services are often offered within the context of a Service Level Agreement (SLA), which ensure the desired Quality of Service (QoS). Aneka, an enterprise Cloud computing solution, harnesses the power of compute resources by relying on private and public Clouds and delivers to users the desired QoS. Its flexible and service based infrastructure supports multiple programming paradigms that make Aneka address a variety of different scenarios: from finance applications to computational science. As examples of scientific computing in the Cloud, we present a preliminary case study on using Aneka for the classification of gene expression data and the execution of fMRI brain imaging workflow.Comment: 13 pages, 9 figures, conference pape

Pump-Probe and Mix-and-Inject Experiments at X-Ray Free Electron Lasers

Time resolved serial femtosecond crystallography (TR-SFX) utilizes X-ray crystallography to visualize the reaction of molecules in real time at the atomic level. Crystals of biological macromolecules are exposed to powerful X-ray pulses. The X-ray radiation emitted by the crystal is then measured by an X-ray sensitive area detector that produces an image called a diffraction pattern. These patterns are analyzed to determine a three-dimensional atomic structure of the biological macromolecule.The ultimate goal of TR-SFX is to make a “molecular movie” that shows the reaction dynamics of a biological process. For this, a reaction is started in a macromolecular crystal and its three-dimensional atomic structures at different time intervals are determined. When these structures are played in a timely order, a molecular movie is recorded. A perfect analogy of this in a real life would be taking pictures of someone dancing, and playing the succession of pictures to observe the dance. TR-SFX is a method that requires an X-ray Free Electron Laser (XFEL). The XFEL produces X-ray pulses of tens of femtosecond duration with 1012 photons per pulse. These pulses are so strong that the crystals are destroyed after being exposed to a single pulse. Since the X-ray pulses ii are so short, diffraction patterns are collected by the detector just before the crystals are destroyed which is called “diffraction before destruction”. Most impressively, at XFELs, each diffraction pattern is obtained from a fresh crystal. As a result, both reversible and non-reversible reactions are placed in an equal footing and can be studied similarly. Pump-probe TR-SFX and mix and inject crystallography (MISC) are two cornerstones of TR-SFX. In pump-probe TR-SFX, photoactive macromolecules within the crystals are activated using an optical laser called the pump, and the reaction is probed by XFEL pulses. Whereas in MISC, biomolecular crystals are mixed with a substrate, and the structural changes are probed by XFEL pulses in a time resolved fashion. This dissertation presents the time-resolved studies of an enzyme called b-lactamase (BlaC) and two photoactive proteins - photoactive yellow protein (PYP) and phytochromes. MISC was used for the study of the enzymatic reaction of BlaC with an antibiotic called Ceftriaxone (CEF). This proof-of-principle experiment conducted at Linac Coherent Light Source (LCLS) operated by Stanford University in Menlo Park, California, showed how CEF binds at the active site of BlaC. Similarly, a pump-probe experiment on PYP was accomplished at the first megahertz XFEL, European XFEL (EuXFEL), in Hamburg, Germany. This experiment was performed to explore the picosecond regime of the photocycle of PYP and test the feasibility of TR-SFX at high repetition rates XFEL. Finally, another pump-probe experiment on phytochromes was conducted at Spring-8 Angstrom Compact free electron Laser (SACLA), in Harima, Japan. With this experiment, we have observed the Z-E isomerization of phytochromes for the first time and determined the previously unknown time-resolved structure at 1ps. iii This dissertation also presents data acquisition techniques and processing methods used at XFELs. It explains methods to analyze millions of patterns obtained during an experiment, with the goal of solving the X-ray structures of different intermediates of the reaction. In summary, my dissertation explains everything from the beginning of the experiment to the production of a molecular movie

Scheduling Heuristics For Executing Scientific Workflows On Homogeneous Clusters With Globallyand Locally-Accessible Persistent Storage

M.S. Thesis. University of Hawaiʻi at Mānoa 2018

improvement of the energy system of a nepali village through innovative exploitation of local resources

Abstract Nepal is one of the less industrialized Countries and does not have fossil fuel reserves. In this scenario, a better exploitation of energy resources is a key factor to start improving the country's overall energy system. For these reasons, the aim of this work, which is the result of a collaboration between two research groups from different countries, is the design of an ORC which recovers the discharged heat by an existing ICE: the integrated system will supply electricity to a small Nepali village, contributing to a little rise of the life standard of a small and poor community

Desert locust and its management in Nepal: a review

Locusts are among the most dangerous agricultural pests. They are a group of short horned grasshoppers belonging to Acrididae family and are hemimetabolous insects. This group of grasshoppers have a unique character of changing habits and behaviors when they aggregate in a group and this habit is catalyzed by different environmental factors. In the adult stage, gregarious locusts migrate from one place to another in a swarm. Desert Locust, Schistocerca gregaria (Forksal), is one of those locusts which cause damage to different types of crop which fly in the direction of wind up to a distance of 150 km. Because of polyphagous feeding habits and swarming in a plague (large group of adults), this pest is considered as the hazardous migratory pest. These pests entered Nepal for the first time in 1962 and then in 1996. In 2020 the pest entered the country from India on three different dates 27th June and continued till 29th (5 districts), 12th July (1 district), and 16th July (2 districts). The swarms migrated to 53 districts and caused the considerable loss in agricultural and field crop in 1118 hectare. These pests are monitored on the basis of environmental factors and many tools and practices such as eLocust3, SMELLS (Soil Moisture for Desert Locust Early Survey), P-locust and SUPARCO Disaster Watch Desert Locust Situation Alert are being used. Their control is critical to food security. Many tools and techniques are integrated for prevention and management of these pests to minimize damage in the existing crops where they migrate. These are physical methods, cultural methods, use of botanicals, green muscle, PAN (phenylacetonitrile) and chemicals. Effective preventive management strategy relies on an improved knowledge of the pest biology, more efficient monitoring and control techniques

A Review Approach on various form of Apriori with Association Rule Mining

Data mining is a computerized technology that uses complicated algorithms to find relationships in large databases Extensive growth of data gives the motivation to find meaningful patterns among the huge data. Sequential pattern provides us interesting relationships between different items in sequential database. Association Rules Mining (ARM) is a function of DM research domain and arise many researchers interest to design a high efficient algorithm to mine ass ociation rules from transaction database. Association Rule Mining plays a important role in the process of mining data for frequent pattern matching. It is a universal technique which uses to refine the mining techniques. In computer science and data min ing, Apriori is a classic algorithm for learning association rules Apriori algorithm has been vital algorithm in association rule mining. . Apriori alg orithm - a realization of frequent pattern matching based on support and confidence measures produced exc ellent results in various fields. Main idea of this algorithm is to find useful patterns between different set of data. It is a simple algorithm yet having man y drawbacks. Many researches have been done for the improvement of this algorithm. This paper sho ws a complete survey on few good improved approaches of Apriori algorithm. This will be really very helpful for the upcoming researchers to find some new ideas from these approaches. The paper below summarizes the basic methodology of association rules alo ng with the mining association algorithms. The algorithms include the most basic Apriori algorithm along with other algorithms such as AprioriTi d, AprioriHybrid

Witnessing the star-formation quenching in L∗L_{*} ellipticals

We study the evolution of $L_{*}$ elliptical galaxies in the color-magnitude diagram in terms of their star-formation history and environment, in an attempt to learn about their quenching process. We have visually extracted 1109 $L_{*}$ galaxies from a sample of 36500 galaxies that were spectroscopically selected from Stripe82 of the Sloan Digital Sky Survey. From this sample we have selected 51 ellipticals based on their surface-brightness profile being well-fitted by a single S$\acute{e}$rsic profile with S$\acute{e}$rsic indices $3<n<6$. Our sample consists of 12 blue-cloud $L_{*}$ ellipticals (BLE), 11 green-valley $L_{*}$ ellipticals (GLE), and 28 red-sequence $L_{*}$ ellipticals (RLE). We find that most of the RLEs and GLEs have been quenched only recently, or are still forming stars, based on their [{O\sc{iii}}] and H$\alpha$ emission, while the BLEs are forming stars vigorously. The star-formation in BLEs is found to be extended over the galaxy and not confined to their central region. In about 40\% of the $L_{*}$ ellipticals (ten BLEs, four GLEs and five RLEs), star-formation quenching seems to have started only recently, based on the lower [{O\sc{iii}}] emission compared to the [{O\sc{ii}}] and H$\alpha$ emission, at a given metallicity. We also find that the galaxy color is correlated with the cosmic-web environment, with the BLEs tending to reside in lower-density regions, the RLEs preferring denser, clustered regions, and the GLEs found in either. One possible scenario is that as the star-forming ellipticals migrate into the clusters, their star formation is suffocated by the hot intra-cluster medium.Comment: Accepted for publication in MNRA

Genome annotation of Anopheles gambiae using mass spectrometry-derived data

BACKGROUND: A large number of animal and plant genomes have been completely sequenced over the last decade and are now publicly available. Although genomes can be rapidly sequenced, identifying protein-coding genes still remains a problematic task. Availability of protein sequence data allows direct confirmation of protein-coding genes. Mass spectrometry has recently emerged as a powerful tool for proteomic studies. Protein identification using mass spectrometry is usually carried out by searching against databases of known proteins or transcripts. This approach generally does not allow identification of proteins that have not yet been predicted or whose transcripts have not been identified. RESULTS: We searched 3,967 mass spectra from 16 LC-MS/MS runs of Anopheles gambiae salivary gland homogenates against the Anopheles gambiae genome database. This allowed us to validate 23 known transcripts and 50 novel transcripts. In addition, a novel gene was identified on the basis of peptides that matched a genomic region where no gene was known and no transcript had been predicted. The amino termini of proteins encoded by two predicted transcripts were confirmed based on N-terminally acetylated peptides sequenced by tandem mass spectrometry. Finally, six sequence polymorphisms could be annotated based on experimentally obtained peptide sequences. CONCLUSION: The peptide sequences from this study were mapped onto the genomic sequence using the distributed annotation system available at Ensembl and can be visualized in the context of all other existing annotations. The strategy described in this paper can be used to correct and confirm genome annotations and permit discovery of novel proteins in a high-throughput manner by mass spectrometry

Efficacy and safety of hydroxychloroquine when added to stable insulin therapy in combination with metformin and glimepiride in patients with type 2 diabetes compare to sitagliptin

Background: The trial was done to evaluate the efficacy and tolerability of hydroxychloroquine when added to stable insulin therapy in combination with metformin and glimepiride in patients with type 2 diabetes (T2DM) compare to sitagliptin.Methods: After two weeks run in period, eligible patients inadequately controlled on long acting, intermediate acting or premixed insulin (HbA1c ≥7.5% and ≤10%), in combination with metformin and glimepiride were randomised 1:1 to the addition of once daily hydroxychloroquine 400mg or sitagliptin 100mg over 24weeks study period. The primary endpoint was HbA1c change from baseline at week 24. Home based glucometer was used to determine finger stick glucose value to detect hypo or hyperglycemia periodically.Results: At 24 weeks, the addition of hydroxychloroquine significantly (p <0.001) reduced HbA1c by 1.3% compared with Sitagliptin which was 0.9%. A greater proportion of patients achieved an HbA1c level <7% while randomised to Hydroxychloroquine as compared with sitagliptin (31 vs. 18% respectively; p <0.001). The addition of hydroxychloroquine significantly (p<0.001) reduced fasting plasma glucose by 31.0mg/dl (vs 23.2mg/dl with sitagliptin) and post prandial plasma glucose by 52.1mg/dl (vs 41mg/dl with sitagliptin) relative to sitagliptin. The difference in mean value of total daily insulin dose showed a highly significant decrease (P <0.0001) from baseline to end of the treatment with hydroxychloroquine i.e. from 41±10.2 to 31.87±16.49 IU as compare to sitagliptin i.e. from 41±10.6 to 37.91±11.71 IU. And also highly significant (P <0.0001) decrease in mean weight was observed at the end of trial with hydroxychloroquine.Conclusions: Hydroxychloroquine decreases HbA1c in patients whose type 2 diabetes is poorly controlled with stable-dose insulin therapy with metformin and glimepiride