• I-TASSER

  • Referenced in 18 articles [sw17207]
  • multiple threading alignments and iterative structural assembly simulations. The function of the protein is then...
  • DYNAMO

  • Referenced in 261 articles [sw01227]
  • DYNAMO (DYNAmic MOdels) was a simulation language and accompanying graphical notation developed within the system ... earliest versions were written in assembly language for the IBM 704, then ... DYNAMO was used for the system dynamics simulations of global resource-depletion reported...
  • ARACHNE

  • Referenced in 9 articles [sw07552]
  • achieves high accuracy by correcting errors before assembly, read merger based on forward-reverse links ... link inconsistency. To test ARACHNE, we created simulated reads providing approximately 10-fold coverage ... chromosomes 21 and 22. The assemblies of these simulated reads yielded nearly complete coverage ... supercontig length of 5143 kb. The assembly accuracy was high, although not perfect: small errors...
  • Cimlib

  • Referenced in 12 articles [sw18094]
  • fully parallel application for numerical simulations based on components assembly. This paper presents CIMLIB with ... that can be organized to build numerical simulation of a certain process. We describe...
  • ISDL

  • Referenced in 10 articles [sw02314]
  • retargetable design tools including compilers and simulators. Such tools enable the design of embedded system ... used to retarget or generate assemblers, disassemblers, compilers, simulators, and hardware models. In addition...
  • Velvet

  • Referenced in 31 articles [sw17026]
  • manipulate de Bruijn graphs for genomic sequence assembly. A de Bruijn graph is a compact ... length in simulations of prokaryotic data and 3-kb N50 on simulated mammalian BACs. When ... simulated results without read-pair information. Velvet represents a new approach to assembly that...
  • SUGGAR

  • Referenced in 15 articles [sw08883]
  • overset grid assembly program designed for moving body simulations that can create an overset composite...
  • SYSWELD

  • Referenced in 2 articles [sw32078]
  • SYSWELD - Welding & Assembly Predictive Simulation. Welding & Assembly simulation minimizes the cost of manufacturing planning...
  • VMD

  • Referenced in 90 articles [sw18651]
  • such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view ... trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical...
  • RSEM

  • Referenced in 12 articles [sw17160]
  • important for quantification with de novo transcriptome assemblies in the absence of sequenced genomes ... intervals, and visualization files and can also simulate RNA-Seq data. In contrast to other ... transcriptome assembler, RSEM enables accurate transcript quantification for species without sequenced genomes. On simulated ... useful for quantification with de novo transcriptome assemblies. In addition, RSEM has enabled valuable guidance...
  • Bambus 2

  • Referenced in 3 articles [sw29700]
  • compare our software to current assemblers using simulated and real data. We demonstrate that ... represents a first step toward automated metagenomic assembly. Availability: Bambus 2 is open source...
  • libDiscretization

  • Referenced in 18 articles [sw22263]
  • libraries and glues the whole simulation framework together. In this discretization library numerical schemes ... trial spaces are found and assembling procedures are defined. Thus, this library uses a suitable...
  • PBSIM

  • Referenced in 3 articles [sw34216]
  • PBSIM: PacBio reads simulator - toward accurate genome assembly. Motivation: PacBio sequencers produce two types ... novo assembly of genomes. Currently, there is no available simulator that targets the specific generation ... normal distribution). We have developed a read simulator, PBSIM, that captures these features using either ... conducted several hybrid error correction and assembly tests for PacBio reads, suggesting that a continuous...
  • SHARCGS

  • Referenced in 8 articles [sw29573]
  • show that 30-mer-based BAC assemblies have N50 sizes >20 kbp for Drosophila ... simulations taking missing reads and wrong base calls into account. We assembled 949,974 contigs...
  • ArchC

  • Referenced in 2 articles [sw07845]
  • automatic generation of high-level SystemC simulators and assemblers. We have used ArchC to synthesize...
  • MuPIF

  • Referenced in 1 article [sw30421]
  • multi-physics and multi-level simulations assembled from independently developed applications (components). The tool provides...
  • CLM

  • Referenced in 2 articles [sw39321]
  • CESM2. We assess an ensemble of simulations, including prescribed and prognostic vegetation state, multiple forcing ... structured dynamic vegetation model (Functionally Assembled Terrestrial Ecosystem Simulator), ozone damage to plants, and fire...
  • PFC

  • Referenced in 14 articles [sw35142]
  • models synthetic materials composed of an assembly of variably-sized rigid particles that interact ... both granular and solid materials. PFC models simulate the independent movement (translation and rotation...
  • automan

  • Referenced in 4 articles [sw39750]
  • automate their computational simulations. In particular the framework facilitates assembling several long-running computations...
  • island

  • Referenced in 1 article [sw32611]
  • environmental variables) given presence-absence data, simulate community assembly, and perform model selection...