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	59
detailed	2
simulations	19
acoustic	2
predictions	3
data-driven	2
modelling	19
gain	2
new	6
insights	2
into	8
biomimetic	2
hydrodynamic	2
mechanisms	3
outcomes	2
support	14
environmentally	2
responsible	2
marine	3
technologies	5
including	39
low-noise	2
propulsors	2
energy-efficient	2
ocean-monitoring	2
platforms	2
project	61
gpu-accelerated	11
deep	18
learning	25
frameworks	8
pytorch	37
tensorflow	20
develop	3
train	3
reinforcement	3
models	23
energy	8
management	4
large-scale	21
data	71
processing	53
numerical	14
computations	4
performed	8
python	170
scientific	15
libraries	30
numpy	27
scipy	20
pandas	23
hpc	30
gpus	8
essential	4
efficient	10
neural	7
network	7
training	19
parallel	39
hyperparameter	5
optimization	8
scenario	3
evaluation	3
under	3
uncertainty	4
workflow	23
leverage	4
batch	19
scheduling	6
system	14
enable	5
reproducible	9
high-throughput	7
experimentation	2
across	15
carbon	2
peak	3
analysis	84
implemented	7
r	97
additional	7
packages	32
statistical	24
methods	18
machine	14
approaches	3
utilizes	4
python-based	11
environment	10
managed	6
miniconda	4
key	7
include	36
developing	5
generative	3
flow	14
3d	6
process	13
involves	9
medical	4
image	14
preprocessing	11
segmentation	6
well	11
plink	8
genotype	3
handling	17
quality	19
control	18
randomized	3
trees	2
algorithm	2
scikit-learn	15
package	11
input	3
output	6
processed	3
astropy	2
do	5
gaussian	14
processes	4
compute	20
functions	8
r-based	2
analytical	4
workflows	21
spatial	13
ecological	2
assessment	3
prioritisation	2
involve	10
large	35
raster	3
datasets	31
distributions	2
future	4
climate	3
associated	8
layers	3
	68
expected	4
gdal	5
alongside	5
analyses	18
manipulation	3
iterative	5
testing	3
research	16
primarily	21
computing	22
ecosystem	6
core	11
matplotlib	15
metagenomic	4
structure	11
prediction	2
sequences	4
current	5
sequence	15
000	3
several	5
million	2
domain	6
filtering	4
clustering	9
primary	9
computational	21
task	4
protein	3
set	4
estimate	3
10	4
full	4
dataset	11
however	2
efficiency	2
plan	4
12	2
nvidia	3
submitted	4
stages	5
approach	2
allows	2
resources	15
while	5
times	3
each	4
stage	2
weeks	2
storage	10
requirements	9
15	2
tb	3
files	12
stored	2
within	9
efficiently	3
scrnaseq	2
analyse	7
interactions	5
human	4
utilise	5
developed	17
pipelines	22
bioinformatic	3
genome	9
sequencing	19
usage	2
samtools	31
minimap2	4
custom	18
scripting	6
bash	9
stack	10
science	4
inference	8
imaging	4
toolkits	4
monai	2
open	13
ai	4
domain-specific	2
loss	2
2d	2
algorithms	8
implementation	4
object	3
detection	6
cellpose	2
cell	15
architectures	10
opencv	7
scikit-image	4
normalization	2
reduction	7
classical	4
divided	2
three	2
computationally	5
intensive	5
high-resolution	3
images	3
geometric	4
improve	4
model	28
gpu	24
accelerated	4
utilize	2
segment	2
nuclei	2
requires	12
acceleration	7
cuda	14
handle	5
validation	2
perform	9
automated	3
conduct	2
comparative	2
vs	2
performance	8
identify	2
most	5
requirements	2
parallelization	2
slurm	14
multiple	16
patient	2
sets	3
total	2
memory	14
high-memory	8
nodes	17
required	19
stacks	3
during	6
access	16
phases	2
cpus	2
mhd	3
code	22
github	13
io	10
written	14
fortran	15
parallelised	8
mpi	14
openmp	8
pseudo-spectral	4
uses	17
radial	2
spherical	3
harmonics	2
fields	2
shell	6
post-processing	7
development	4
networks	6
time-series	4
text	7
monte	3
carlo	3
techniques	8
quantification	8
levels	3
extensive	4
experiments	9
embedding	2
sizes	4
fusion	2
strategies	5
tasks	8
ablation	2
studies	2
calibration	2
computation	6
evaluate	4
anything	2
sam	2
vision	2
transformers	6
combine	2
llm	2
generated	4
includes	3
cuda-enabled	2
scale	5
fine-tuning	3
multi-modal	4
feature	5
extraction	8
high-performance	7
sufficient	2
vram	2
fast	3
capacity	4
intermediate	5
checkpoints	2
experiment	2
outputs	13
transcriptomics	7
proteomic	2
bulk	4
single	6
ranger	8
seurat	12
scanpy	13
integration	11
trajectory	2
facility	11
cellranger	8
fastqc	18
fastq	3
comet	6
beta	3
anaconda	12
java	8
relies	4
both	6
because	2
containers	4
distributed	4
cluster	7
still	2
necessary	4
nextflow	2
containerised	3
cutadapt	3
amplicon	3
multiqc	10
modules	12
modular	4
blast	9
ansys	22
workbench	7
very	3
fine	2
mesh	4
rna-seq	9
single-cell	8
scrna-seq	6
pipeline	13
bioinformatics	21
trimmomatic	3
adapter	2
trimming	3
star	17
hisat2	7
read	12
alignment	16
reference	5
genomes	3
transcript	3
featurecounts	4
salmon	11
kallisto	2
followed	2
downstream	13
bioconductor	3
deseq2	4
dimensionality	5
cell-type	2
annotation	9
addition	3
following	6
julia	12
matlab	68
capabilities	4
rna	10
long-read	4
ont	2
structural	7
variants	3
conducted	6
appropriate	2
bamtools	7
bedtools	16
study	5
regions	2
file	8
ondemand	6
signac	3
scenic	2
tidyverse	7
utilises	3
11	2
designed	2
gpu-l	3
framework	8
utilising	2
docker	3
ensure	7
reproducibility	2
configured	2
operations	2
directly	2
engineering	4
sensor	2
graphs	2
geopandas	4
complex	6
specifically	5
graph	2
attention	2
autoencoders	2
"	2
mixed	2
open-source	6
commercial	3
consisting	2
amd	2
2025	2
synthesis	2
hardware	2
given	2
substantial	2
amount	4
cpu	15
part	9
make	6
more	8
applications	5
systems	6
learn	3
independent	3
workload	7
serial	2
arrays	4
modest	2
out	5
benchmarking	3
runs	9
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
typical	4
netcdf	7
geospatial	3
xarray	2
rioxarray	2
comparison	2
existing	3
products	3
memory-intensive	5
dna	5
dorado	2
assembly	5
verkko	2
routinely	2
analysed	2
variation	2
snps	2
established	5
languages	2
visualisation	17
differential	10
gene	5
expression	10
widely	2
adopted	2
functional	11
enrichment	3
pathway	2
databases	2
executed	9
interactive	3
multi-core	3
moderate	2
workloads	9
execution	7
resource	2
scripts	20
samples	5
transcriptomic	2
qc	7
merging	2
trim	3
galore!	2
sorting	2
indexing	2
samtools	2
picard	9
ecosystems	2
anndata	2
applied	4
cell-cell	2
interaction	6
developmental	2
compare	2
programmes	2
design	3
test	3
sample	5
largely	2
cover	3
mechanical	2
fea	2
only	2
lammps	9
density	5
theory	5
dft	4
molecular	11
dynamics	8
md	3
reduced	2
potential	3
mapping	8
natural	2
nbo	3
relevant	4
capture	2
source	10
heat	3
lstm	2
cross-validation	2
search	3
over	7
preparation	3
rasterio	2
hdf5	6
integrate	2
earth	3
incorporates	2
satellite	2
imagery	2
optical	2
interpretation	3
areas	2
pre-processing	3
repeated	2
derivatives	2
computer	4
then	4
detect	2
suitable	3
bcftools	15
built	4
biocmanager	3
provide	5
functionality	4
genomic	2
change	2
normalisation	6
correction	2
space	4
scvi	4
harmony	4
squidpy	2
cell2location	3
environments	8
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	3
mode	2
hybrid	4
fluid	6
calling	8
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
jupyter	10
form	2
genes	2
reads	5
megahit	4
microbial	2
common	2
jax	6
optimisation	4
singularity	5
apptainer	3
ml	2
solver	6
spins	2
navier-stokes	2
consists	3
case	4
four	2
you	2
must	2
suite	7
phylogenetic	2
eggnog-mapper	2
making	4
bigstatsr	2
bigsnpr	2
integrated	3
genetics	4
rapid	2
through	6
compute-intensive	2
generation	8
shared	2
statically	2
compiled	3
binaries	2
simulating	2
simulation	10
two	2
language	3
main	6
consist	2
offline	2
than	2
long	6
login	2
together	4
benchmark	2
its	2
interface	2
academic	3
module	2
licensed	2
cores	3
larger	2
node	4
approximately	4
ram	5
requirement	2
later	2
machine-learning	3
components	2
behaviour	2
depending	3
size	3
loading	2
complete	4
neural-network	2
longer	2
inputs	3
parameters	4
statistics	5
summary	3
tables	2
plots	5
trained	2
diagnostics	2
linux	10
bam	3
handing	2
viewing	2
interrogation	2
aligned	2
benchmarks	2
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
spades	5
along	5
microscopy	2
added	2
programme	2
genomics	9
raw	2
matrix	3
modeling	2
sctcr	2
clonotype	2
torch	3
h5py	2
seaborn	3
torchvision	2
shapely	2
team	4
git	7
virtual	2
milopy	2
tracking	2
mainly	9
produce	4
frames	4
chains	2
counting	3
rstudio	7
ggplot2	3
activity	2
objects	2
toolkit	5
quantum	9
state	3
art	2
fft	3
rk4	2
sampling	4
mcmc	3
*	2
force	3
field	2
bespoke	4
openmm	2
gromacs	5
dynamics	3
free	3
potentials	3
discrete	2
selection	4
estimated	2
tensors	3
signal	2
dynamic	2
quantitative	2
accuracy	3
robustness	2
proposed	2
liana	3
basic	8
sas	2
molecules	2
espresso	6
calculations	6
vasp	6
integrates	2
orca	5
modern	2
yolo	3
classification	3
gnss	2
maintained	2
laboratory	3
gps	2
positioning	2
stations	2
supports	4
monitoring	2
ssh	2
user	2
transient	3
students	3
fsl	5
their	3
carried	2
format	3
impact	3
solvers	4
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
combination	3
electronic	5
reaction	2
energetics	2
employ	3
basis	2
mpi-based	3
particle	2
fluent	10
transfer	2
multiphase	4
kinetic	2
parameter	3
estimation	2
coupling	2
paraview	5
automation	3
remote	2
conda	7
potentially	3
notebook	4
visualise	4
results	3
notebooks	3
production	2
conjunction	2
video	2
depth	2
initial	4
found	2
higher	2
24gb	2
about	2
takes	2
right	2
maximum	2
order	5
highly	2
states	2
www	14
unix	3
manager	3
small	2
programming	6
hugging	3
face	3
scalable	2
publications	2
cpu-intensive	2
pytorch-based	2
alphafold3	2
throughout	2
minimum	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
details	3
amrex-combustion	2
pelelmex	2
2024	2
range	3
amber	2
coupled	3
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
dependencies	2
targeted	2
fastp	4
hostile	2
taxonomic	2
profiling	3
metaphlan	2
humann	2
biobakery	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
align	2
rnaseq	4
technology	2
types	2
skills	2
nanopore	2
being	3
tophat	3
analysing	2
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
related	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
freesurfer	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
10x	2
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