Explore our community of HPC Projects and users, grouped by software titles or methods they are using in their research.

This mapping of software to research activity is generated by a word frequency analysis of the software and processes each active, published, HPC Project has submitted.

The wordcloud graphic above is a dynamic representation of the frequency analysis of the software used by our published HPC research projects.

We also maintain a directory of published projects which have used HPC facilities at Newcastle University.

Software Keyword	Frequency
used	39
simulations	12
modelling	8
new	4
into	5
support	10
technologies	2
including	26
project	41
gpu-accelerated	8
deep	12
learning	18
frameworks	4
pytorch	23
tensorflow	17
develop	2
train	2
reinforcement	3
models	15
energy	6
management	3
large-scale	13
data	47
processing	32
numerical	9
computations	3
performed	4
python	137
scientific	9
libraries	19
numpy	16
scipy	10
pandas	12
hpc	20
gpus	6
essential	4
efficient	8
neural	5
network	5
training	13
parallel	25
hyperparameter	2
optimization	4
under	2
uncertainty	2
workflow	15
leverage	3
batch	9
scheduling	4
system	11
enable	4
reproducible	3
high-throughput	6
across	4
peak	2
utilizes	3
python-based	6
environment	6
managed	3
miniconda	4
key	6
include	16
developing	4
generative	2
flow	7
3d	4
process	9
involves	7
medical	4
image	12
preprocessing	4
segmentation	6
research	10
primarily	12
computing	14
ecosystem	4
core	6
additional	5
matplotlib	7
metagenomic	3
structure	9
sequences	3
current	3
sequence	10
several	3
domain	3
analyses	12
filtering	4
clustering	2
primary	5
computational	13
task	2
protein	2
set	4
estimate	3
10	4
full	3
dataset	3
however	2
efficiency	2
plan	4
nvidia	3
stages	3
allows	2
resources	8
while	3
times	2
each	2
stage	2
storage	7
requirements	4
15	2
files	7
within	7
efficiently	3
scikit-learn	9
associated	5
utilise	3
developed	13
pipelines	13
bioinformatic	3
analysis	47
genome	7
sequencing	10
packages	21
usage	2
samtools	26
minimap2	3
custom	12
scripting	4
bash	8
r	80
compute	9
	46
stack	6
science	3
inference	3
imaging	4
toolkits	4
monai	2
open	11
ai	3
loss	2
functions	4
algorithms	5
implementation	3
object	3
detection	4
cellpose	2
cell	5
architectures	5
opencv	6
scikit-image	4
classical	3
methods	11
divided	2
three	2
computationally	3
intensive	3
high-resolution	2
images	3
geometric	2
improve	2
model	14
gpu	14
accelerated	2
segment	2
requires	7
acceleration	2
cuda	10
handle	4
iterative	3
large	19
datasets	16
perform	7
automated	2
conduct	2
comparative	2
performance	6
most	5
requirements	2
parallelization	2
slurm	9
multiple	7
patient	2
sets	2
memory	9
high-memory	4
nodes	11
required	12
stacks	3
during	3
access	15
phases	2
cpus	2
mhd	2
code	20
github	11
io	10
written	12
fortran	15
parallelised	7
mpi	11
openmp	8
pseudo-spectral	4
uses	14
radial	2
spherical	3
harmonics	2
shell	5
post-processing	4
development	3
networks	4
time-series	3
text	5
monte	2
carlo	2
techniques	5
quantification	3
levels	3
extensive	3
experiments	3
embedding	2
sizes	4
fusion	2
strategies	4
tasks	7
studies	2
calibration	2
computation	5
evaluate	2
anything	2
transformers	4
generated	2
includes	3
machine	8
workflows	10
involve	4
scale	3
fine-tuning	2
multi-modal	3
feature	3
extraction	5
high-performance	4
vram	2
fast	3
capacity	2
intermediate	4
outputs	7
transcriptomics	5
proteomic	2
bulk	3
single	2
cellranger	7
fastqc	15
fastq	2
comet	5
beta	3
anaconda	11
java	8
both	6
because	2
distributed	2
cluster	6
still	2
necessary	4
nextflow	2
containerised	2
cutadapt	2
amplicon	3
multiqc	8
modules	12
modular	4
blast	8
addition	2
following	4
julia	11
matlab	61
capabilities	4
bioinformatics	16
rna	6
rna-seq	3
long-read	3
bamtools	7
bedtools	14
study	3
regions	2
file	5
ondemand	6
seurat	4
signac	2
scenic	2
tidyverse	7
utilises	2
designed	2
gpu-l	3
framework	4
utilising	2
docker	3
ensure	6
reproducibility	2
configured	2
operations	2
directly	2
pipeline	12
engineering	4
sensor	2
graphs	2
geopandas	2
complex	4
specifically	3
graph	2
"	2
allow	3
it	7
intended	5
gaussian	13
chemistry	2
where	5
expect	2
few	2
minutes	2
hours	3
time	8
dna	5
dorado	2
open-source	4
assembly	4
verkko	2
routinely	2
structural	3
snps	2
established	3
languages	2
analyse	3
quality	8
control	7
alignment	9
statistical	14
visualisation	11
differential	2
gene	3
expression	2
widely	2
adopted	2
downstream	9
functional	7
enrichment	2
databases	2
executed	7
interactive	3
facility	6
multi-core	3
cpu	8
moderate	2
workloads	5
execution	2
resource	2
scripts	15
future	2
samples	2
design	3
test	3
sample	4
largely	2
ansys	19
fea	2
lammps	9
implemented	3
bcftools	15
built	4
biocmanager	3
provide	2
functionality	4
genomic	2
processed	2
change	2
over	4
analytical	2
xshells	2
c	24
method	2
solve	2
magnetohydrodynamics	2
equations	3
geometry	4
fourier	2
library	7
fftw	6
employed	3
parallelisation	2
done	3
mode	2
hybrid	4
openfoam	9
code_saturne	2
senga-ops	2
in-house	8
infrastructure	2
intend	2
jupyter	5
part	7
form	2
phylogenetic	2
eggnog-mapper	2
making	4
bigstatsr	2
bigsnpr	2
integrated	2
genetics	4
plink	7
rapid	2
through	4
genotype	2
generation	4
shared	2
two	2
netcdf	5
linux	10
bam	2
handing	2
viewing	2
interrogation	2
aligned	2
benchmarks	2
vcf	2
handling	8
normalisation	2
variant	9
calls	5
gatk	13
mutect2	2
calling	7
indel	3
mutserve	2
mitochondrial	2
caller	3
snv	2
haplocheck	2
contamination	2
checker	2
main	3
added	2
programme	2
torch	3
torchvision	2
environments	2
team	4
runs	5
mainly	7
produce	4
frames	2
plots	4
arrays	2
relevant	2
quantum	8
state	3
art	2
fft	3
rk4	2
sampling	2
mcmc	3
*	2
force	2
field	2
toolkit	3
bespoke	4
openmm	2
gromacs	4
molecular	7
dynamics	3
free	3
potentials	3
simulation	7
signal	2
optimisation	2
quantitative	2
accuracy	3
robustness	2
dft	2
molecules	2
espresso	5
calculations	3
case	3
vasp	5
integrates	2
orca	5
yolo	2
classification	2
git	5
user	2
space	2
memory-intensive	2
enables	2
applications	2
bwa	14
picard	8
vep	6
well	7
reads	3
call	3
input	2
interpretation	2
output	4
group	2
sniffles	2
callers	2
alongside	2
annotation	5
investigate	3
high	6
high-dimensional	2
workload	3
significant	2
more	4
stan	2
notebook	4
visualise	4
results	3
jax	4
production	2
source	7
conjunction	2
generate	5
initial	4
tests	6
found	2
higher	2
ram	3
approximately	2
about	2
long	5
node	3
takes	2
right	2
final	3
take	2
maximum	2
order	4
electronic	4
states	2
www	14
unix	3
manager	3
small	2
amount	2
programming	5
basic	6
finite	3
difference	2
reacting	2
mesh	2
amr	2
high-speed	2
cfd	6
problems	2
industry	2
wide	2
variety	2
command-line	4
along	4
acceptable	2
members	3
utilities	5
working	4
solvers	3
rocket	5
dynamics	6
solver	3
center	2
sciences	2
lawrence	2
berkeley	2
national	2
laboratory	2
further	3
details	3
amrex-combustion	2
pelelmex	2
screening	2
clusters	2
gfortran	4
potentially	2
paraview	4
compiler	6
package	7
tested	2
fluent	9
dedalus	2
request	2
us	2
after	2
combined	2
programs	2
combination	2
generic	3
mapping	5
sandia	2
ngs	2
wes	3
bio	2
read	7
projects	2
qc	6
stata	5
rstudio	5
keras	4
intel	5
studio	11
cmake	2
gnu	2
compile	2
employ	2
ranger	2
	2
fluid	4
decomposition	2
parallelism	2
emacs	2
statistics	3
jdk	2
release	2
gcc	6
preferably	2
aligner	3
compiled	2
perl	8
out	2
star	14
various	2
compiling	2
dependencies	2
targeted	2
fastp	4
human	3
hostile	2
bowtie2	7
bacterial	3
taxonomic	2
profiling	3
metaphlan	2
humann	2
biobakery	2
suite	6
megahit	2
bwa-mem	3
checkm	2
metabat2	2
dada2	3
kraken2	3
mothur	3
s-andrews	2
en	4
linux_x64_install	2
html	5
broadinstitute	3
tag	2
arq5x	2
bedtools2	2
htseq	3
readthedocs	2
cran	2
r-project	2
bin	2
ubuntu	4
fullreadme	2
hc	2
en-us	2
articles	3
360036194592-getting-started-with-gatk4	2
downloads	2
salmon	9
align	2
rnaseq	4
hisat2	5
deseq2	2
technology	2
types	2
skills	2
impact	2
computer	3
do	3
nanopore	2
being	3
selection	3
conda	5
bowtie	3
tophat	3
workbench	5
make	4
analysing	2
integration	3
multi-omic	2
typical	2
visualization	3
interactions	2
genomics	8
comsol	3
simulator	2
pip	2
complete	2
population	4
due	2
go	2
featurecounts	2
hdf5	4
gdal	2
python3	2
snptest	2
number	2
agisoft	2
spatial	5
macs2	2
spaceranger	3
pre-processing	2
density	2
theory	2
conducted	3
machine-learning	2
systems	5
automation	2
together	3
aimpro	2
gnuplot	2
jmol	2
phd	2
students	2
nbo	2
useful	2
hugging	2
face	2
tumours	2
transient	2
mpi-based	2
shared-memory	2
nucleotide	2
spades	4
mtdna	2
variants	2
tool	2
doi	2
trinity	2
deeplabcut	2
trimmomatic	2
trim	2
afni	2
fsl	4
freesurfer	2
their	2
producing	2
alignments	2
provides	2
range	2
genetic	2
very	2
many	2
high-quality	2
multiphysics	2
singularity	2
stable	2
fmrib	3
docs	3
ab	2
initio	2
nmr	3
visual	2
cfx	2
multiphase	2
coupled	2
ggplot2	2
mkl	2
toolboxes	2
scikit	2
dsi-studio	2
labsolver	2
modules	2
surfer	2
mgh	2
harvard	2
fslwiki	2
vcftools	5
10x	2
scrna-seq	2
scanpy	2
muon	2
epitrace	2
pseudotime	2
epi2me	2
nf-core	2
scnanoseq	2
recent	2
admixture	3
phylogenomics	3
iqtree	3
beast	4
supports	2
ncbi	2
nih	2