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
starccm	3
used	68
detailed	2
simulations	24
acoustic	2
predictions	5
data-driven	2
modelling	21
gain	2
new	6
insights	2
into	8
biomimetic	2
hydrodynamic	2
mechanisms	4
outcomes	2
support	16
environmentally	2
responsible	2
marine	3
technologies	8
including	45
low-noise	2
propulsors	2
energy-efficient	2
ocean-monitoring	2
platforms	2
project	69
primarily	28
r	104
research	17
package	16
computational	24
workflow	27
includes	5
calculation	2
information	3
variation	3
distances	2
analysis	92
geometric	6
analyses	20
minimum	3
trees	3
related	3
methods	22
	74
hpc	35
facility	12
computationally	6
intensive	7
execution	8
simulation	12
bayesian	2
mcmc	4
production	3
runs	13
multiple	18
large	43
involve	11
independent	5
across	17
datasets	39
comparing	2
their	4
resulting	2
summary	4
statistics	6
distributions	3
gpu-accelerated	14
deep	23
learning	30
frameworks	9
pytorch	45
tensorflow	20
develop	3
train	4
reinforcement	3
models	28
energy	9
management	4
large-scale	26
data	79
processing	62
numerical	15
computations	4
performed	8
python	189
scientific	19
libraries	34
numpy	31
scipy	24
pandas	28
gpus	9
essential	5
efficient	10
neural	11
network	9
training	24
parallel	42
hyperparameter	8
optimization	10
scenario	3
evaluation	7
under	4
uncertainty	4
leverage	4
batch	22
scheduling	6
system	14
enable	5
reproducible	10
high-throughput	7
experimentation	2
carbon	2
peak	3
implemented	7
additional	9
packages	38
statistical	27
machine	15
approaches	3
utilizes	4
python-based	14
environment	11
managed	8
miniconda	4
key	7
include	43
developing	5
generative	4
flow	14
3d	6
process	13
involves	10
medical	4
image	14
preprocessing	12
segmentation	6
well	12
plink	8
genotype	3
handling	18
quality	20
control	19
randomized	3
algorithm	2
scikit-learn	17
input	3
output	6
processed	4
astropy	2
do	5
gaussian	14
processes	4
compute	27
functions	8
r-based	2
analytical	4
workflows	26
spatial	17
ecological	2
assessment	3
prioritisation	3
raster	3
future	4
climate	5
associated	8
layers	3
expected	6
gdal	5
alongside	6
manipulation	3
iterative	5
testing	3
computing	27
ecosystem	7
core	12
matplotlib	18
metagenomic	4
structure	11
prediction	2
sequences	4
current	5
sequence	16
000	4
several	5
million	2
domain	6
filtering	4
clustering	11
primary	9
task	4
protein	4
set	4
estimate	3
10	5
full	4
dataset	12
however	2
balance	2
efficiency	2
plan	4
12	2
nvidia	3
submitted	5
stages	5
approach	2
allows	2
resources	16
while	7
times	3
each	4
stage	2
weeks	2
storage	10
requirements	9
15	2
tb	3
files	12
stored	2
within	9
efficiently	6
scrnaseq	2
analyse	7
interactions	5
human	5
utilise	5
developed	17
pipelines	23
bioinformatic	5
genome	10
sequencing	20
usage	2
samtools	31
minimap2	4
custom	21
scripting	9
bash	12
stack	10
science	4
inference	12
imaging	4
toolkits	4
monai	2
open	14
ai	4
domain-specific	2
specialized	2
loss	2
2d	2
algorithms	8
implementation	4
object	3
detection	8
cellpose	2
cell	19
architectures	11
opencv	7
scikit-image	4
normalization	2
reduction	7
classical	4
divided	2
three	2
high-resolution	3
images	3
intensity	2
improve	4
model	33
gpu	34
accelerated	4
utilize	2
segment	2
nuclei	5
requires	12
acceleration	9
cuda	15
handle	5
validation	2
perform	10
automated	5
conduct	3
comparative	2
vs	3
performance	9
identify	3
most	5
biomarkers	2
requirements	2
parallelization	2
slurm	16
patient	2
sets	4
total	2
memory	14
high-memory	9
nodes	19
required	19
stacks	3
during	6
access	16
phases	2
cpus	2
mhd	3
code	25
github	14
io	11
written	16
fortran	17
parallelised	8
mpi	14
openmp	8
pseudo-spectral	4
uses	20
radial	2
spherical	3
harmonics	2
fields	2
shell	6
post-processing	9
development	6
networks	8
time-series	4
text	7
monte	3
carlo	3
techniques	8
quantification	9
levels	3
extensive	4
experiments	13
embedding	2
sizes	4
fusion	2
strategies	5
tasks	9
ablation	3
studies	4
agent	2
calibration	2
visualisation	19
computation	7
evaluate	5
anything	2
sam	3
vision	2
transformers	8
multimodal	2
combine	2
llm	2
generated	4
cuda-enabled	4
scale	7
fine-tuning	5
multi-modal	4
feature	6
extraction	8
high-performance	7
sufficient	2
vram	2
fast	3
capacity	4
intermediate	5
checkpoints	2
experiment	5
outputs	16
transcriptomics	7
proteomic	2
bulk	4
single	9
ranger	9
seurat	13
scanpy	18
integration	13
trajectory	2
cellranger	8
fastqc	18
fastq	3
comet	7
beta	3
anaconda	12
java	8
relies	4
included	2
both	7
because	2
containers	8
distributed	7
cluster	7
still	2
necessary	4
nextflow	2
containerised	3
cutadapt	3
amplicon	3
multiqc	10
modules	14
modular	4
blast	9
ansys	22
workbench	7
very	3
fine	3
mesh	4
rna-seq	9
single-cell	8
scrna-seq	6
pipeline	14
bioinformatics	22
trimmomatic	3
adapter	2
trimming	3
star	17
hisat2	7
read	12
alignment	17
reference	6
genomes	3
transcript	3
featurecounts	4
salmon	11
kallisto	2
followed	2
downstream	14
bioconductor	5
deseq2	4
dimensionality	5
cell-type	3
annotation	10
range	6
fastp	5
kraken2	4
spades	6
prokka	2
addition	3
following	6
julia	12
matlab	69
capabilities	4
rna	11
long-read	4
ont	2
structural	8
variants	3
conducted	7
appropriate	2
bamtools	7
bedtools	16
study	5
regions	2
file	8
ondemand	6
signac	3
scenic	2
tidyverse	8
utilises	3
11	2
designed	2
gpu-l	3
framework	13
utilising	2
docker	3
ensure	7
reproducibility	2
configured	2
operations	3
directly	2
engineering	4
sensor	2
graphs	2
geopandas	5
complex	6
specifically	5
graph	2
attention	2
autoencoders	2
"	2
mixed	2
open-source	8
commercial	3
consisting	2
amd	2
2025	2
synthesis	3
hardware	2
given	2
substantial	2
amount	4
cpu	19
part	9
make	7
more	8
applications	5
systems	6
learn	3
workload	8
serial	2
arrays	6
modest	2
out	6
benchmarking	3
allow	3
it	12
intended	5
published	2
et	2
al	2
solves	2
transport	3
chemistry	2
where	6
expect	2
normal	2
few	2
minutes	3
hours	5
time	9
generate	9
high-dimensional	5
interpolation	2
visualization	5
gridded	2
typical	5
netcdf	8
geospatial	3
xarray	4
rioxarray	2
comparison	2
existing	3
era5	2
products	3
memory-intensive	7
dna	5
dorado	2
assembly	5
verkko	2
routinely	2
analysed	2
snps	2
coupled	4
ice	2
mass	2
dependencies	4
thermodynamic	2
weather	2
stations	3
dynamics	9
grid	2
parameter	6
established	5
languages	2
differential	11
gene	5
expression	11
widely	2
adopted	2
functional	12
enrichment	3
pathway	3
databases	2
executed	9
interactive	4
multi-core	4
moderate	2
workloads	13
resource	2
version-controlled	2
scripts	24
samples	5
transcriptomic	3
qc	7
merging	2
trim	3
galore!	2
removal	2
sorting	2
indexing	2
samtools	2
picard	9
ecosystems	2
anndata	3
applied	4
cell-cell	2
interaction	7
developmental	2
compare	2
programmes	2
density	6
theory	6
basis	3
rdkit	3
generation	9
force	4
field	3
selection	5
regression	3
design	3
test	3
sample	5
largely	2
cover	3
mechanical	2
fea	2
only	2
lammps	9
dft	4
molecular	12
md	3
reduced	2
potential	3
mapping	8
natural	2
nbo	3
relevant	4
capture	2
git	11
virtual	5
environments	13
recognised	4
public	4
bin2cell	4
squidpy	5
milor	4
milopy	5
scvi-tools	5
linux	11
desktop	2
rstudio	8
automation	4
activity	3
cheminformatics	2
docking	2
compounds	2
jupyter	13
notebooks	5
source	11
heat	3
lstm	2
cross-validation	2
search	3
over	7
preparation	3
approximately	5
30	2
matrix	4
specialised	2
licensed	3
—	2
rasterio	2
hdf5	6
integrate	2
earth	4
observation	2
incorporates	2
satellite	2
imagery	2
optical	2
interpretation	3
areas	2
pre-processing	3
repeated	4
derivatives	2
computer	4
then	4
detect	2
suitable	3
solver	7
bcftools	15
built	5
biocmanager	3
provide	5
functionality	4
genomic	2
change	2
normalisation	6
correction	2
space	4
scvi	5
harmony	5
cell2location	3
remote	3
shetran	2
wrapper	2
analysing	3
tracking	4
readthedocs	3
en	5
xshells	2
c	26
spectral	2
method	3
solve	2
magnetohydrodynamics	2
equations	3
rotating	2
geometry	4
fourier	2
library	8
fftw	7
employed	3
parallelisation	2
done	4
mode	2
hybrid	4
fluid	6
supporting	2
optimisation	7
manage	2
calling	8
diffusion-based	2
representations	2
openfoam	9
code_saturne	2
senga-ops	2
in-house	9
infrastructure	2
script	2
manipulated	2
final	4
secondary	2
tests	7
take	3
personal	2
days	2
intend	2
form	2
genes	2
reads	6
megahit	4
microbial	2
common	2
jax	6
singularity	6
apptainer	4
ml	2
spins	2
navier-stokes	2
consists	3
case	4
four	2
you	2
must	2
suite	7
phylogenetic	2
eggnog-mapper	2
fsl	6
freesurfer	3
mrtrix3	2
through	9
conda	9
making	4
bigstatsr	2
bigsnpr	2
integrated	3
genetics	4
rapid	2
compute-intensive	2
shared	2
statically	2
compiled	3
binaries	2
simulating	2
two	2
language	5
main	8
consist	2
offline	2
scheduler	3
than	2
long	6
login	2
together	4
benchmark	3
its	2
interface	2
academic	3
module	2
cpu-	2
cores	3
larger	3
node	4
ram	5
communication	2
requirement	2
later	2
machine-learning	4
components	2
behaviour	2
interactively	2
depending	3
size	3
loading	2
complete	4
neural-network	2
longer	2
sensitive	2
inputs	3
parameters	4
tables	2
plots	5
trained	3
diagnostics	2
bam	3
handing	2
viewing	2
interrogation	2
aligned	2
benchmarks	3
vcf	2
variant	9
calls	5
gatk	13
mutect2	2
indel	3
mutserve	2
mitochondrial	2
caller	3
snv	2
haplocheck	2
contamination	2
checker	2
aligners	2
bwa	15
bowtie	4
along	5
microscopy	2
added	2
programme	2
omics	2
survival	2
genomics	10
raw	3
modeling	2
sctcr	2
clonotype	2
torch	3
h5py	2
seaborn	3
torchvision	2
shapely	2
team	4
mainly	11
produce	4
frames	4
chains	2
single-nucleus	2
counting	3
ggplot2	3
matrices	2
gene-expression	2
objects	2
toolkit	5
quantum	9
setups	2
state	3
art	2
fft	3
rk4	2
sampling	4
convolutional	2
yolo	4
classification	4
*	2
bespoke	4
openmm	2
gromacs	5
dynamics	3
free	3
potentials	3
discrete	2
configurations	2
estimated	2
tensors	3
signal	2
dynamic	2
quantitative	2
accuracy	3
robustness	2
proposed	2
cellphonedb	2
liana	4
basic	9
sas	2
molecules	2
espresso	6
calculations	6
vasp	6
integrates	2
orca	5
modern	2
gnss	2
maintained	2
laboratory	3
gps	2
positioning	2
supports	4
monitoring	2
ssh	2
user	2
activities	2
cpu-based	2
accelerate	2
pytorch-based	3
details	4
transient	3
students	3
carried	3
format	3
hugging	5
face	5
handled	2
weights	2
multi-gpu	2
operators	2
order	6
flood	2
global	2
hydrological	2
impact	3
solvers	4
scenarios	2
transformer-based	2
enables	2
ensuring	2
iteration	2
vep	6
call	3
plus	2
rmats	2
splicing	2
chip-seq	2
bowtie2	9
macs2	3
group	2
sniffles	2
callers	2
investigate	4
high	6
significant	3
bacterial	4
conversion	2
subread	2
container	2
stan	3
operating	2
characteristics	2
combination	3
electronic	5
reaction	2
energetics	2
employ	3
mpi-based	3
particle	2
fluent	10
transfer	2
multiphase	4
kinetic	2
estimation	2
coupling	2
paraview	5
potentially	3
notebook	4
visualise	4
results	3
10x	3
starsolo	2
cellbender	2
highly	3
conjunction	2
video	2
depth	2
initial	4
found	2
higher	2
24gb	2
about	2
takes	2
right	2
maximum	2
states	2
www	14
unix	3
manager	3
small	2
programming	6
scalable	2
publications	2
cpu-intensive	2
alphafold3	2
throughout	2
utilised	2
finite	3
difference	2
reacting	2
amr	2
high-speed	2
flows	2
cfd	6
problems	2
industry	2
immune	2
receptor	2
due	3
determine	2
wide	2
variety	2
command-line	4
acceptable	2
members	3
utilities	5
working	4
rocket	5
center	2
sciences	2
lawrence	2
berkeley	2
national	2
further	3
amrex-combustion	2
pelelmex	2
2024	2
amber	2
clusters	3
screening	2
gfortran	4
compiler	6
tested	2
dedalus	2
request	2
us	2
after	2
combined	2
programs	2
generic	3
sandia	2
ngs	2
wes	3
bio	2
projects	2
stata	5
keras	4
intel	5
studio	11
cmake	2
gnu	2
compile	2
	2
decomposition	2
parallelism	2
emacs	2
jdk	2
release	2
gcc	6
preferably	2
aligner	3
perl	8
various	2
compiling	2
targeted	2
hostile	2
taxonomic	2
profiling	3
metaphlan	2
humann	2
biobakery	2
bwa-mem	3
checkm	2
metabat2	2
dada2	3
mothur	3
s-andrews	2
linux_x64_install	2
html	5
broadinstitute	3
tag	2
arq5x	2
bedtools2	2
htseq	3
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
align	2
rnaseq	4
technology	2
types	2
skills	2
nanopore	2
being	3
tophat	3
multi-omic	2
comsol	3
simulator	2
pip	2
population	4
sweeps	2
go	2
same	2
python3	2
olga	2
snptest	2
number	2
agisoft	2
spaceranger	3
aimpro	2
gnuplot	2
jmol	2
phd	2
useful	2
tumours	2
define	2
shared-memory	2
nucleotide	2
simple	2
mtdna	2
tool	2
doi	2
identification	2
trinity	2
deeplabcut	2
features	2
afni	2
producing	2
alignments	2
provides	2
genetic	2
many	2
high-quality	2
multiphysics	2
stable	2
fmrib	3
docs	3
ab	2
initio	2
nmr	3
visual	2
cfx	2
calculate	2
mkl	2
toolboxes	2
scikit	2
dsi-studio	2
labsolver	2
modules	2
surfer	2
mgh	2
harvard	2
fslwiki	2
vcftools	5
muon	2
epitrace	2
pseudotime	2
epi2me	2
nf-core	2
scnanoseq	2
recent	2
admixture	3
phylogenomics	3
iqtree	3
beast	4
ncbi	2
nih	2