Set Up and Calibration of a Spatial Tool for Simulating River Discharge of Western Java in Recent Decades: Preliminary Results and Assessments

This paper discusses a study of the application of global spatiotemporal climate datasets and the hydrological model STREAM (Spatial Tools for River Basin Environmental Analysis and Management Options). In the study, set up and calibration of STREAM for the reconstruction of monthly discharge for several locations in the western part of Java, Indonesia, for the period 1983 -2002 are carried out. The set up includes the preparation of monthly precipitation and temperature datasets, a digital elevation model of the domain being studied, and maps of land cover and soil water holding capacity. Discharge observations from six stations located mostly in the upper parts of major watersheds in the domain are used to calibrate the model by comparing simulated and observed discharge variables. The model performs reasonably well. Comparison between computed and observed mean monthly discharges yield correlation coefficients ranging from 0.72 to 0.93. The computed mean annual discharge in five out of six observation stations ranges between -8 and 5% with respect to the mean annual observed discharge. This study offers a tool which can be used for reconstructing historical discharg

Spatial Decision Assistance of Watershed Sedimentation (SDAS): Development and Application

This paper discusses the development and application of a spatial tool for erosion modeling named Spatial Decision Assistance of Watershed Sedimentation (SDAS). SDAS computes export (yield) of sediment from watershed as product of erosion rate and sediment delivery ratio (SDR). The erosion rate is calculated for each raster grid according to a digital elevation model, soil, rain fall depth, and land cover data using the Universal Soil Loss Equation. SDR calculation is carried out for each spatial unit. A spatial unit is the smallest sub-watershed considered in the model and generated according to the TauDEM algorithm. The size of one spatial unit is assigned by the user as the minimum number of raster grids. SDR is inversely proportional to sediment resident time and controlled by rainfall, slope, soil, and land cover. Application of SDAS is demonstrated in this paper by simulating the spatial distribution of the annual sediment yield across the Citarum watershed in the northwest of Java, Indonesia. SDAS calibration was carried out based on sediment discharge observations from the upper catchment. We considered factors for hillslope flow depth and for actual and effective rainfall duration to fit the computed sediment yield to the observed sediment discharge. The computed sediment yield agreed with the observation data with a 7% mean relative accuracy

Simulation of River Discharges in Major Watersheds of Northwestern Java From 1901 To 2006

This study is intended to simulate the river discharges in major watersheds of northwestern Java, Indonesia. The five largest watersheds are considered: Ciujung, Cisadane, Ciliwung, Citarum, and Cimanuk. The simulation period covers the 20th century and early 21st century, from January 1901 to June 2006, at a monthly time step. Discharge simulation was carried out using STREAM (Spatial Tools for River Basins and Environmental and Analysis of Management Option). The input data for the simulation are climate (precipitation and temperature), land cover and topographic data. Setup and analysis of input data are also part of this study. The Mann-Kendall test and linear regression were used to detect trends. Temperature datasets show statistically significant increasing trends for all periods and areas. Significant increasing trends of precipitation occurred in the latest 16-year period (1990-2006) in hilly and middle areas. A positive trend of simulated discharge is seen in all watersheds and periods. They are only significant for Ciujung (periods of 1950-2006 and 1975-2006), Cisadane (periods of 1950-2006 and 1990-2006), and Ciliwung (periods of 1950-2006, 1975-2006, and 1990- 2006). The most noteworthy trend is seen in the 1990-2006 period. Over the course of the 20th and early decade of the 21st century, monthly discharges have increased by 3% to 9%

Phased nanopore assembly with Shasta and modular graph phasing with GFAse

Reference-free genome phasing is vital for understanding allele inheritance and the impact of single-molecule DNA variation on phenotypes. To achieve thorough phasing across homozygous or repetitive regions of the genome, long-read sequencing technologies are often used to perform phased de novo assembly. As a step toward reducing the cost and complexity of this type of analysis, we describe new methods for accurately phasing Oxford Nanopore Technologies (ONT) sequence data with the Shasta genome assembler and a modular tool for extending phasing to the chromosome scale called GFAse. We test using new variants of ONT PromethION sequencing, including those using proximity ligation, and show that newer, higher accuracy ONT reads substantially improve assembly quality

Set Up and Calibration of a Spatial Tool for Simulating Latest Decades’ Flow Discharges of the Western Java: Preliminary Results and Assessments

This paper discusses a study of application of global spatio-temporal climate data sets and a hydrological model operated in Spatial Tools for River Basin Environmental Analysis and Management (STREAM). The study investigates reconstruction of monthly hydrographs across several selected points of the western part of Java, Indonesia for the period 1983-2002. Prior to the reconstruction, set up and calibration are carried out. The set up includes preparation of monthly precipitation and temperature data set, digital elevation model of the domain being studied and their compilation with land cover map. Discharge observations from six stations located mostly at the upper parts of major watersheds in the domain are used to calibrate the model. It is found that the model performs results with acceptable agreement. Comparison between computed and observed monthly average discharges correlate quite well with coefficient ranging from 0.72 to 0.93. The accuracy of computed total annual average discharge in five out of six observation stations is within the range of 7%. Optimum setting of calibration parameters is discovered. This study offers scheme for reconstructing historical discharge in paleo-climate perspective and future scenario for predicting local effect of global climate change, given the predicted climate data sets and geographic setting (i.e. topography and land cover)

Set Up and Calibration of a Spatial Tool for Simulating River Discharge of Western Java in Recent Decades: Preliminary Results and Assessments

This  paper  discusses  a  study  of  the  application  of  global  spatiotemporal climate datasets and the hydrological model STREAM   (Spatial Tools for River Basin Environmental Analysis and Management Options). In the study, set up and calibration  of STREAM for  the reconstruction of monthly discharge for several locations in the western part of Java, Indonesia, for the period 1983 -2002 are carried out. The set up includes the preparation of monthly precipitation and temperature datasets, a digital elevation model of the domain being studied, and maps of land cover and soil water holding capacity. Discharge observations from  six  stations  located  mostly  in  the  upper  parts  of  major  watersheds  in  the domain  are  used  to  calibrate  the  model  by  comparing  simulated  and  observed discharge variables. The model performs reasonably well.  Comparison  between computed and observed mean monthly discharges yield correlation coefficients ranging from 0.72 to 0.93. The  computed mean annual discharge in five out of six  observation  stations  ranges  between  -8  and  5%  with  respect  to  the  mean annual  observed  discharge.  This  study  offers  a  tool  which  can  be  used  for reconstructing historical discharg

KAITAN ANTARA ASPEK PENENTUAN POSISI, PEMETAAN, DAN SISTEM INFORMASI GEOGRAFIS SERTA PERMASALAHANNYA DENGAN SUPLEMEN ELEMEN-ELEMEN SISTEM KOORDINAT

Penentuan posisi, pemetaan dan Sistem Informasi Geografis (SIG) merupakan keping-keping mosaik pada suatu permasalah geodesi dan geomatika. Antara keping satu dan lainnya pasti saling berkaitan. Masalahnya tidak semua orang menganggap antara keping tersebut sebagai-kesatuan. Sebagai seorang geodet harus dapat memandang sebuah permasalah godesi dan geomatika sebagai suatu aspek penentuan posisi, pemetaan, dan SlG sebagai mosaik yang saling mendukung. Pada makalah ini disajikan sebuah studi kasus tentang permodelan erosi, sehingga terlihat jelas hubungan dan peran antara ketiga aspek tersebut. Selain itu, dari ketidakseragaman data masukan dalam penentuan erosi dapat dikaji pula mengenai variasi sistem koordinat setiap data serta proses penyeragamannya guna keberhasilan proses selanjutnya

A draft human pangenome reference

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample