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	2
used	22
simulations	8
modelling	8
new	4
into	3
support	8
including	20
project	29
gpu-accelerated	8
deep	10
learning	15
frameworks	2
pytorch	20
tensorflow	16
develop	2
train	2
reinforcement	3
models	13
energy	6
management	2
large-scale	9
data	36
processing	21
numerical	6
computations	2
performed	3
python	123
scientific	8
libraries	12
numpy	15
scipy	9
pandas	11
hpc	11
gpus	5
essential	2
efficient	6
neural	5
network	3
training	10
parallel	18
hyperparameter	2
optimization	3
under	2
uncertainty	2
workflow	10
batch	4
scheduling	3
system	8
enable	3
high-throughput	6
across	3
peak	2
research	9
primarily	11
computing	10
ecosystem	3
core	5
additional	5
matplotlib	7
metagenomic	3
structure	8
sequences	2
current	2
sequence	8
several	3
domain	2
analyses	10
filtering	3
clustering	2
primary	3
computational	10
protein	2
set	4
estimate	2
10	4
full	2
dataset	2
however	2
efficiency	2
plan	3
nvidia	2
stages	2
allows	2
resources	4
while	2
each	2
stage	2
storage	6
requirements	4
15	2
files	4
within	5
efficiently	3
scikit-learn	8
associated	3
uses	10
model	8
development	3
involves	6
networks	3
time-series	3
text	4
analysis	31
medical	2
image	8
techniques	3
quantification	2
multiple	5
levels	2
requires	4
extensive	3
experiments	3
architectures	4
sizes	2
fusion	2
computationally	2
intensive	2
tasks	4
include	9
studies	2
calibration	2
gpu	10
computation	4
anything	2
transformers	4
imaging	2
stack	4
includes	3
machine	7
toolkits	2
workflows	7
involve	3
large	15
preprocessing	2
fine-tuning	2
multi-modal	3
feature	3
extraction	3
datasets	11
high-performance	4
vram	2
fast	3
intermediate	3
outputs	6
cellranger	4
fastqc	16
comet	3
beta	3
required	8
	34
anaconda	11
java	8
both	6
because	2
distributed	2
cluster	6
still	2
necessary	3
bioinformatics	13
rna	5
custom	8
pipelines	8
sequencing	6
long-read	2
utilises	2
gpu-l	3
framework	3
utilising	2
cuda	9
docker	3
ensure	5
perform	5
operations	2
directly	2
pipeline	9
engineering	4
sensor	2
graphs	2
geopandas	2
complex	3
specifically	3
graph	2
dna	2
nodes	8
dorado	2
developed	10
open-source	3
packages	17
genome	5
assembly	4
verkko	2
routinely	2
structural	3
snps	2
design	2
test	2
sample	3
workloads	3
largely	2
ansys	20
fea	2
implemented	3
bash	7
samtools	22
bcftools	13
r	70
scripts	8
built	4
biocmanager	3
tidyverse	5
provide	2
functionality	4
modular	2
executed	3
genomic	2
over	4
time	6
methods	5
analytical	2
code	17
written	8
fortran	12
xshells	2
c	23
magnetohydrodynamics	2
equations	3
spherical	2
geometry	4
fourier	2
library	6
fftw	6
employed	3
parallelisation	2
done	3
mpi	10
hybrid	4
openmp	6
openfoam	9
code_saturne	2
senga-ops	2
in-house	6
utilise	2
infrastructure	2
cpu	4
intend	2
jupyter	4
part	6
making	4
key	3
bigstatsr	2
bigsnpr	2
genetics	4
plink	6
rapid	2
through	3
quality	6
control	6
generation	4
statistical	11
high-memory	2
multi-core	2
shared	2
downstream	7
two	2
parallelised	6
netcdf	5
matlab	57
julia	7
main	3
visualisation	8
added	2
programme	2
torch	3
torchvision	2
environments	2
team	4
*	2
open	8
force	2
field	2
toolkit	3
bespoke	2
openmm	2
gromacs	3
molecular	7
dynamics	2
free	3
potentials	3
dft	2
quantum	6
espresso	5
calculations	3
case	2
vasp	4
simulation	4
environment	5
integrates	2
functions	2
plots	2
orca	6
git	5
investigate	3
high	4
performance	2
process	5
high-dimensional	2
workload	2
significant	2
memory	5
capabilities	2
more	4
access	12
jax	3
production	2
following	3
source	7
output	2
linux	8
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	2
take	2
runs	3
hours	2
maximum	2
order	4
images	2
www	15
most	4
unix	2
well	5
slurm	5
manager	2
small	2
amount	2
programming	5
basic	5
compute	7
finite	3
difference	2
reacting	2
flow	4
github	11
amr	2
high-speed	2
cfd	5
industry	2
it	4
wide	2
variety	2
command-line	4
along	4
facility	4
algorithms	3
acceptable	2
members	3
utilities	5
modules	10
working	4
intended	3
solvers	2
rocket	5
dynamics	5
solver	3
lammps	8
center	2
sciences	2
lawrence	2
berkeley	2
national	2
laboratory	2
further	3
details	3
amrex-combustion	2
io	9
pelelmex	2
gfortran	4
potentially	2
paraview	4
compiler	5
package	7
tested	2
fluent	9
gaussian	11
pseudo-spectral	3
dedalus	2
request	2
sandia	2
ngs	2
wes	2
bio	2
read	7
projects	3
qc	6
alignment	8
variant	6
annotation	4
vep	4
gatk	9
stata	5
rstudio	5
keras	4
intel	5
studio	11
cmake	2
gnu	2
compile	2
python-based	2
opencv	5
employ	2
ai	2
cell	3
ranger	2
	2
fluid	2
3d	2
decomposition	2
emacs	2
statistics	3
implementation	2
jdk	2
release	2
picard	6
gcc	6
preferably	2
aligner	2
compiled	2
perl	8
out	2
star	12
indel	2
caller	2
bedtools	13
compiling	2
dependencies	2
targeted	2
amplicon	2
miniconda	3
fastp	4
human	3
hostile	2
bowtie2	7
bacterial	3
taxonomic	2
functional	5
profiling	3
metaphlan	2
humann	2
biobakery	2
suite	5
megahit	2
mapping	4
bamtools	5
bwa-mem	3
checkm	2
metabat2	2
detection	2
dada2	3
kraken2	3
blast	7
mothur	3
s-andrews	2
en	4
linux_x64_install	2
html	5
broadinstitute	3
tag	2
arq5x	3
bedtools2	3
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
analyse	2
salmon	9
align	2
rnaseq	3
reads	2
hisat2	5
visualise	2
deseq2	2
technology	2
types	2
skills	2
developing	3
impact	2
computer	3
do	3
nanopore	2
being	3
multiqc	7
selection	2
conda	5
bowtie	3
tophat	3
workbench	5
bwa	10
make	4
analysing	2
calling	4
integration	3
multi-omic	2
typical	2
visualization	3
interactions	2
genomics	6
handle	3
comsol	3
simulator	2
scikit-image	3
segmentation	3
pip	2
mainly	4
where	3
complete	2
scripting	2
calls	3
ondemand	2
notebook	3
go	2
featurecounts	2
hdf5	4
gdal	2
python3	2
shell	2
interactive	2
accuracy	2
electronic	3
snptest	2
number	2
agisoft	2
handling	5
science	2
spatial	4
transcriptomics	3
file	2
macs2	2
spaceranger	2
conducted	2
machine-learning	2
systems	3
together	3
aimpro	2
generic	2
gnuplot	2
jmol	2
phd	2
students	2
nbo	2
useful	2
hugging	2
face	2
bioinformatic	2
icem	2
nucleotide	2
spades	4
call	2
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
range	2
genetic	2
very	2
many	2
high-quality	2
singularity	2
stable	2
fmrib	3
docs	3
ab	2
initio	2
nmr	3
visual	2
cfx	2
multiphase	2
ggplot2	2
mkl	2
stacks	2
toolboxes	2
scikit	2
dsi-studio	2
labsolver	2
surfer	2
mgh	2
harvard	2
fslwiki	2
vcftools	4
recent	2
population	3
admixture	3
phylogenomics	3
iqtree	3
beast	4
ncbi	2
nih	2