• ParEGO

  • Referenced in 52 articles [sw10968]
  • tight evaluation budget -- tens or hundreds of function evaluations, rather than thousands. In this paper ... surrogate model of the search landscape after every function evaluation, which it uses to estimate...
  • PuFFIN

  • Referenced in 2 articles [sw22390]
  • relies on a set of nucleosome ”landscapefunctions at different resolution levels: each function represents...
  • FRAGSTATS

  • Referenced in 16 articles [sw31496]
  • designed to compute a wide variety of landscape metrics for categorical map patterns.The original software ... version 4 (v4.2) has essentially the same functionality as version 3, but with ... variety of sampling methods for analyzing sub-landscapes...
  • FLoWS

  • Referenced in 1 article [sw24492]
  • terrestrial components of a landscape based on hydrologic processes. This functionality allows for spatial analysis...
  • TopoZeko

  • Referenced in 1 article [sw33485]
  • function extends existing MATLAB plotting routines and allows for high-quality 3-D landscape visualization ... generated in the code. Additionally a simple function to calculate the position ... visualize the daily insolation/shadow cycle over a landscape...
  • RMBase

  • Referenced in 2 articles [sw27671]
  • RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data ... known about the modified positions and their functions. Recently, various high-throughput modification sequencing methods ... mirlab.sysu.edu.cn/rmbase/), to decode the genome-wide landscape of RNA modifications identified from high-throughput ... will help expand our understanding of potential functions of RNA modifications...
  • Fastsg

  • Referenced in 5 articles [sw18350]
  • Sparse Grids. In a complex processor landscape dominated by multi-and many-core processors, simplifying ... highly tuned library functions. In this paper we present fastsg, an optimized library...
  • APLEpy

  • Referenced in 5 articles [sw04913]
  • collection of Python modules that provides the functionality of an algebraic modeling and programming software ... here a recent review of the software landscape for such products. APLEpy does not only...
  • SHGO

  • Referenced in 1 article [sw26954]
  • expensive function evaluations efficiently which is especially suitable to applications such as energy landscape exploration ... SHGO algorithm will always outperform TGO on function evaluations if the objective function is Lipschitz...
  • Ocelet

  • Referenced in 1 article [sw20629]
  • landscapes. It is characterised by the use of interaction graphs (graphs with interaction functions...
  • GATE

  • Referenced in 6 articles [sw06442]
  • design using a relatively low number of function evaluations. The heart of the algorithm ... which was initially calibrated using a Gaussian landscape generator as test case, is shown...
  • SMEAGOL

  • Referenced in 5 articles [sw33755]
  • molecular electronics in atomically generated orbital landscapes. Ab initio computational methods for electronic transport ... junctions, which integrates the nonequilibrium Green’s function method with density functional theory. This...
  • SiMRiv

  • Referenced in 1 article [sw15872]
  • package SiMRiv. Provides functions to generate and analyze individual-based spatially-explicit simulations of multi ... state movements in heterogeneous landscapes, based on ”resistance” rasters. Although originally conceived and designed...
  • Rnall

  • Referenced in 1 article [sw23119]
  • algorithm for predicting RNA local secondary structural landscape in genomes. BACKGROUND: The information ... help retrieve biologically important motifs and study functions of RNA molecules. Most of the current ... further introduced the concept of energy landscape for illustrating RNA LSS, which may facilitate...
  • miRNet

  • Referenced in 1 article [sw29355]
  • designed for creation, customization, visual exploration and functional interpretation of miRNA–target interaction networks ... allows researchers to easily navigate the complex landscape of miRNA–target interactions to obtain deep ... miRNA–target networks for visual exploration and functional analysis from different types of data inputs...
  • movecost

  • Referenced in 1 article [sw32585]
  • Paths Related to Human Movement Across the Landscape. Provides the facility to calculate non-isotropic ... number of human-movement-related cost functions that can be selected by the user...
  • MITIE

  • Referenced in 1 article [sw34895]
  • observed complexity of the transcriptional landscape, pose profound computational challenges for transcriptome reconstruction. Results ... reconstruction and quantification. We define a likelihood function based on the negative binomial distribution...
  • MUFFINN

  • Referenced in 1 article [sw23967]
  • genes. An important observation from cancer mutation landscapes is mutational convergence into cancer-associated pathways ... genes but also those of neighbors in functional networks, MUFFINN (MUtations For Functional Impact...
  • Pylogeny

  • Referenced in 1 article [sw28977]
  • bindings to the libpll phylogenetic C library. Functionality also exists in the framework to execute ... this library: Generate and maintain phylogenetic tree landscapes. Construct and analyse heuristic methods to search...
  • GAMES

  • Referenced in 1 article [sw17427]
  • methods have the potential for changing the landscape of biomedical science, but at the same ... which is insufficiently annotated and of difficult functional comprehension to end users. Results: We developed...