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	55
detailed	2
simulations	17
acoustic	2
predictions	2
data-driven	2
modelling	14
gain	2
new	6
insights	2
into	7
biomimetic	2
hydrodynamic	2
mechanisms	3
outcomes	2
support	12
environmentally	2
responsible	2
marine	3
technologies	3
including	33
low-noise	2
propulsors	2
energy-efficient	2
ocean-monitoring	2
platforms	2
project	52
gpu-accelerated	9
deep	14
learning	20
frameworks	5
pytorch	28
tensorflow	19
develop	3
train	2
reinforcement	3
models	19
energy	6
management	4
large-scale	17
data	58
processing	43
numerical	12
computations	4
performed	6
python	154
scientific	12
libraries	24
numpy	22
scipy	17
pandas	18
hpc	26
gpus	8
essential	4
efficient	10
neural	6
network	5
training	15
parallel	30
hyperparameter	4
optimization	7
scenario	2
under	3
uncertainty	3
workflow	20
leverage	3
batch	13
scheduling	6
system	13
enable	4
reproducible	7
high-throughput	6
across	7
carbon	2
peak	3
utilizes	3
python-based	7
environment	9
managed	5
miniconda	4
key	7
include	26
developing	5
generative	2
flow	13
3d	6
process	11
involves	9
medical	4
image	13
preprocessing	7
segmentation	6
randomized	2
trees	2
algorithm	2
scikit-learn	12
package	9
input	3
output	5
processed	3
astropy	2
packages	28
do	4
gaussian	14
processes	4
compute	13
functions	7
implemented	5
r-based	2
analytical	3
workflows	15
spatial	9
ecological	2
assessment	2
prioritisation	2
involve	6
handling	12
large	26
raster	2
datasets	23
future	4
climate	2
associated	7
layers	3
	60
expected	3
r	88
gdal	4
analysis	64
alongside	3
analyses	18
manipulation	2
iterative	4
testing	2
research	14
primarily	15
computing	18
ecosystem	4
core	6
additional	5
matplotlib	12
metagenomic	3
structure	11
prediction	2
sequences	4
current	4
sequence	12
several	5
million	2
domain	5
filtering	4
clustering	5
primary	8
computational	17
task	3
protein	3
set	4
estimate	3
10	4
full	3
dataset	9
however	2
efficiency	2
plan	4
nvidia	3
submitted	2
stages	4
approach	2
allows	2
resources	12
while	4
times	3
each	4
stage	2
weeks	2
storage	9
requirements	6
15	2
tb	3
files	11
within	9
efficiently	3
scrnaseq	2
analyse	6
interactions	4
human	4
utilise	4
developed	15
pipelines	16
bioinformatic	3
genome	9
sequencing	14
usage	2
samtools	29
minimap2	4
custom	14
scripting	5
bash	8
stack	7
science	4
inference	5
imaging	4
toolkits	4
monai	2
open	13
ai	4
loss	2
2d	2
algorithms	7
implementation	3
object	3
detection	5
cellpose	2
cell	8
architectures	6
opencv	6
scikit-image	4
normalization	2
reduction	4
classical	4
methods	12
divided	2
three	2
computationally	5
intensive	5
high-resolution	3
images	3
geometric	4
improve	3
model	20
gpu	18
accelerated	2
utilize	2
segment	2
requires	12
acceleration	3
cuda	11
handle	5
validation	2
perform	8
automated	2
conduct	2
comparative	2
vs	2
performance	7
most	5
requirements	2
parallelization	2
slurm	12
multiple	11
patient	2
sets	3
memory	12
high-memory	6
nodes	15
required	17
stacks	3
during	5
access	15
phases	2
cpus	2
mhd	3
code	22
github	13
io	10
written	12
fortran	15
parallelised	7
mpi	14
openmp	8
pseudo-spectral	4
uses	16
radial	2
spherical	3
harmonics	2
shell	6
post-processing	7
development	3
networks	5
time-series	3
text	5
monte	2
carlo	2
techniques	6
quantification	7
levels	3
extensive	3
experiments	6
embedding	2
sizes	4
fusion	2
strategies	4
tasks	8
ablation	2
studies	2
calibration	2
computation	6
evaluate	3
anything	2
sam	2
transformers	4
generated	3
includes	3
cuda-enabled	2
machine	11
scale	4
fine-tuning	2
multi-modal	3
feature	3
extraction	6
high-performance	5
sufficient	2
vram	2
fast	3
capacity	4
intermediate	5
checkpoints	2
experiment	2
outputs	10
transcriptomics	6
proteomic	2
bulk	4
single	3
cellranger	7
fastqc	18
fastq	3
comet	6
beta	3
anaconda	11
java	8
relies	2
both	6
because	2
containers	2
distributed	4
cluster	6
still	2
necessary	4
nextflow	2
containerised	3
cutadapt	3
amplicon	3
multiqc	10
modules	12
modular	4
blast	8
ansys	22
workbench	7
very	3
fine	2
mesh	4
facility	9
rna-seq	8
single-cell	3
scrna-seq	4
pipeline	13
bioinformatics	19
quality	14
control	14
trimmomatic	3
adapter	2
trimming	3
star	17
hisat2	6
read	12
alignment	14
reference	4
genomes	2
transcript	3
featurecounts	4
salmon	10
kallisto	2
followed	2
downstream	12
statistical	20
bioconductor	2
deseq2	4
ranger	4
seurat	6
scanpy	5
dimensionality	2
cell-type	2
annotation	9
addition	3
following	6
julia	11
matlab	67
capabilities	4
rna	6
long-read	4
ont	2
structural	7
variants	3
conducted	5
appropriate	2
bamtools	7
bedtools	15
study	3
regions	2
file	8
ondemand	6
signac	2
scenic	2
tidyverse	7
utilises	2
11	2
designed	2
gpu-l	3
framework	5
utilising	2
docker	3
ensure	7
reproducibility	2
configured	2
operations	2
directly	2
engineering	4
sensor	2
graphs	2
geopandas	4
complex	5
specifically	3
graph	2
attention	2
"	2
part	9
make	6
more	8
applications	5
systems	6
learn	3
allow	3
it	12
intended	5
et	2
al	2
solves	2
transport	3
chemistry	2
where	6
expect	2
few	2
minutes	3
hours	4
time	8
generate	8
high-dimensional	3
visualization	5
typical	3
netcdf	6
xarray	2
rioxarray	2
comparison	2
existing	3
products	2
memory-intensive	4
dna	5
dorado	2
open-source	5
assembly	5
verkko	2
routinely	2
snps	2
established	4
languages	2
visualisation	14
differential	5
gene	3
expression	5
widely	2
adopted	2
functional	11
enrichment	2
databases	2
executed	8
interactive	3
multi-core	3
cpu	11
moderate	2
workloads	7
execution	3
resource	2
scripts	17
samples	4
qc	7
merging	2
trim	3
galore!	2
sorting	2
indexing	2
samtools	2
picard	9
design	3
test	3
sample	4
largely	2
cover	2
mechanical	2
fea	2
only	2
lammps	9
density	5
theory	5
dft	4
molecular	11
dynamics	8
md	2
reduced	2
interaction	4
potential	2
mapping	7
nbo	3
relevant	3
capture	2
bcftools	15
built	4
biocmanager	3
provide	4
functionality	4
genomic	2
change	2
over	5
normalisation	4
integration	4
space	3
harmony	2
environments	6
xshells	2
c	25
spectral	2
method	3
solve	2
magnetohydrodynamics	2
equations	3
rotating	2
geometry	4
fourier	2
library	7
fftw	7
employed	3
parallelisation	2
done	3
mode	2
hybrid	4
fluid	6
source	9
calling	8
openfoam	9
code_saturne	2
senga-ops	2
in-house	8
infrastructure	2
then	2
script	2
final	4
amount	3
secondary	2
tests	7
well	8
take	3
personal	2
days	2
intend	2
jupyter	7
form	2
common	2
jax	6
optimisation	3
benchmarking	2
arrays	3
singularity	4
apptainer	2
ml	2
commercial	2
solver	6
spins	2
navier-stokes	2
consists	2
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
plink	7
rapid	2
through	5
genotype	2
generation	7
shared	2
statically	2
compiled	3
binaries	2
two	2
language	2
main	5
workload	5
consist	2
offline	2
long	6
login	2
together	4
benchmark	2
runs	8
its	2
interface	2
academic	2
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
preparation	2
complete	4
longer	2
inputs	2
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
megahit	3
along	5
microscopy	2
added	2
programme	2
torch	3
h5py	2
seaborn	2
torchvision	2
shapely	2
team	4
mainly	7
produce	4
frames	3
chains	2
toolkit	4
quantum	9
state	3
art	2
fft	3
rk4	2
sampling	2
mcmc	3
*	2
force	2
field	2
bespoke	4
openmm	2
gromacs	4
dynamics	3
free	3
potentials	3
simulation	8
signal	2
quantitative	2
accuracy	3
robustness	2
proposed	2
liana	2
basic	7
rstudio	6
sas	2
molecules	2
espresso	6
calculations	5
vasp	6
integrates	2
orca	5
yolo	3
classification	2
gnss	2
maintained	2
laboratory	3
gps	2
positioning	2
stations	2
supports	4
earth	2
monitoring	2
git	6
ssh	2
user	2
transient	3
students	3
fsl	5
their	3
carried	2
out	4
format	2
enables	2
vep	6
reads	4
call	3
interpretation	2
chip-seq	2
plus	2
splicing	2
group	2
sniffles	2
callers	2
investigate	4
high	6
significant	3
bowtie2	8
bacterial	4
conversion	2
subread	2
counting	2
container	2
suitable	2
stan	3
combination	3
electronic	5
reaction	2
energetics	2
employ	3
basis	2
mpi-based	3
particle	2
fluent	10
heat	2
transfer	2
multiphase	4
kinetic	2
parameter	2
estimation	2
coupling	2
paraview	5
automation	3
remote	2
conda	7
potentially	3
notebook	4
visualise	4
results	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	5
pytorch-based	2
alphafold3	2
throughout	2
hdf5	5
tensors	2
matrix	2
minimum	2
utilised	2
finite	3
difference	2
reacting	2
amr	2
high-speed	2
flows	2
cfd	6
problems	2
industry	2
determine	2
wide	2
variety	2
command-line	4
acceptable	2
members	3
utilities	5
working	4
solvers	3
rocket	5
center	2
sciences	2
lawrence	2
berkeley	2
national	2
further	3
details	3
amrex-combustion	2
pelelmex	2
screening	2
clusters	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
impact	2
computer	3
nanopore	2
being	3
selection	3
tophat	3
analysing	2
multi-omic	2
genomics	8
comsol	3
simulator	2
pip	2
population	4
due	2
go	2
same	2
python3	2
olga	2
snptest	2
number	2
agisoft	2
macs2	2
spaceranger	3
pre-processing	2
aimpro	2
gnuplot	2
jmol	2
related	2
phd	2
useful	2
hugging	2
face	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
range	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
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
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