cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10426435
title: Project Section: Searching for Mutations Leading to Isoniazid Resistance in TB (HackBio)

description: Introduction

Tuberculosis (TB) remains a global health concern, and the emergence of drug-resistant strains poses a significant challenge to effective treatment. Isoniazid is a key first-line drug used in the treatment of TB, and resistance to this drug can compromise the success of therapy. 

This project aims to identify and characterise genetic mutations associated with isoniazid resistance in Mycobacterium tuberculosis, the causative agent of TB. 

Datasets: Here

Task:



Given the datasets above, perform the complete variant calling and annotation pipeline to specifically identify the following known mutations in Mycobacterium tuberculosis (against Isoniazid). 

Provide pretty IGV visualisation of mutations in katG sequences (Position: 2156111 - 2153889) across all the samples. N/B: katG mutations are prevalent in isoniazid resistance.

Also, explore associated biological pathways to understand the molecular mechanisms of isoniazid resistance.


Expected Output:

Kindly submit a comprehensive project report, including methods, results, and interpretations.
DOI: 10.5281/zenodo.10886725
title: Project Section: Searching for Mutations Leading to Isoniazid Resistance in TB (HackBio)

description: Introduction

Tuberculosis (TB) remains a global health concern, and the emergence of drug-resistant strains poses a significant challenge to effective treatment. Isoniazid is a key first-line drug used in the treatment of TB, and resistance to this drug can compromise the success of therapy. 

This project aims to identify and characterise genetic mutations associated with isoniazid resistance in Mycobacterium tuberculosis, the causative agent of TB. 

Datasets: Here

Task:



Given the datasets above, perform the complete variant calling and annotation pipeline to specifically identify the following known mutations in Mycobacterium tuberculosis (against Isoniazid). 

Provide pretty IGV visualisation of mutations in katG sequences (Position: 2156111 - 2153889) across all the samples. N/B: katG mutations are prevalent in isoniazid resistance.

Also, explore associated biological pathways to understand the molecular mechanisms of isoniazid resistance.


Expected Output:

Kindly submit a comprehensive project report, including methods, results, and interpretations.
DOI: 10.23728/b2share.b18d8ab706224ca5bbc4e01de5bc4c3f
title: Air quality data from the LIFE+RESPIRA project in Pamplona, Spain: NO2 (01h CET) (clipped GeoTIFF)

description: Clipped GeoTIFF file including interpolated air quality data from the LIFE+RESPIRA project (http://www.liferespira.eu/) in Pamplona, Spain, with measures of nitrogen dioxide, aggregated by hour (01h CET).
DOI: 10.23728/b2share.ee0b4d360a27440ab8ba01d554a647f9
title: Air quality data from the LIFE+RESPIRA project in Pamplona, Spain: O3 in 2015 (01h CET) (interpolated GeoTIFF)

description: GeoTIFF file including interpolated air quality data from the LIFE+RESPIRA project (http://www.liferespira.eu/) in Pamplona, Spain, with measures of ozone during 2015, aggregated by hour (01h CET).
DOI: 10.23728/b2share.a263d1d9bb3f4e2fb4ba383cfb030c78
title: Air quality data from the LIFE+RESPIRA project in Pamplona, Spain: NO2 (01h CET) (clipped PNG)

description: PNG image representing clipped interpolated air quality data from the LIFE+RESPIRA project (http://www.liferespira.eu/) in Pamplona, Spain, with measures of nitrogen dioxide, aggregated by hour (01h CET).
DOI: 10.23728/b2share.a08fd9b7d200427b872a69f848095460
title: Statistics of star formation and magnetic seeding

description: Tabular data for the cosmic star formation history in cosmological simulations, and of the relative magnetisation output of stellar activity. For meaning of the models please refer to http://cosmosimfrazza.myfreesites.net/magnetic-models and Vazza et al. 2017 CQG "Simulations of extragalactic magnetic fields and of their observables" http://iopscience.iop.org/article/10.1088/1361-6382/aa8e60
1st column: cosmic time [Gyr]; 2nd: average cosmic star formation rate [Msol/yr/Mpc^3]; 3rd column: magnetic field at the injection (in 83^3 kpc^3), in proper Gauss; 4th column=average magnetic field injected in the cosmic volume [G].
DOI: 10.23728/b2share.cf49996d869540b6aefc9a06ee5082f5
title: Simulated cosmic volume - Primordial magnetic seeding models.

description: These are 2 subsets (300^3 cells each) derived from larger 1024^3 cosmological MHD simulations produced using ENZO on Piz-Daint (CSCS) by F.Vazza& collaborators. In these "primordial" models we impose an initial seed field of ~1nG (comoving) at the begin of the simulation (z=38). 
In the "P" run we initialised a uniform field aligned along the X,Y,Z direction, while the "Pz2" run is for a field aligned with the Z-direction only.
These dataset are extracted around a massive cluster at z=0, and give gas density, Dark Matter density, temperature and magnetic field components in cgs units [g/cm^3, K and Gauss]. Each cell has a comoving size of 83.3 kpc. 
The data are written in HDF5 format (https://support.hdfgroup.org/HDF5/). 
We additionally provide also .fits maps of the X and Z projection across the box, showing the volume weighted mean density, DM density, temperature, |B| and Bz. 
For more details on the simulations please refer to 
http://cosmosimfrazza.myfreesites.net/magnetic-models
Vazza et al. 2017 CQG (http://iopscience.iop.org/article/10.1088/1361-6382/aa8e60)
DOI: 10.23728/b2share.1b3b57a62ea64e2d8d48c3fca5ddd39d
title: Simulated cosmic volume - astrophysical seeding scenario

description: These are 3 subsets (300^3 cells each) derived from larger 1024^3 cosmological MHD simulations produced using ENZO on Piz-Daint (CSCS) by F.Vazza& collaborators. In these "astrophysical" models we impose a negligibly small initial seed field, and later seed magnetic fields from the feedback activity of star forming particles and/or supermassive BH particles in ENZO. 
In the "CSF3" run magnetic fields are only seeded by stellar feedback, assuming that 10% of the thermal feedback energy goes into magnetic field energy.
In the "CSFBH2" run we also include seeding from BH (1% of energy goes into magnetic feedback).
In the "CSFBH5" run the magnetic feedback efficiency from BH particles is increased to 10%.
The star formation is implemented following Kravtsov+2003, while the BH particle are injected at z=4 (M=10^5 Msol) within halos and then evolve following the implementation by Kim+2011. The run are radiative and evolve also 7 chemical species. 
These dataset are extracted around a massive cluster at z=0, and give gas density, Dark Matter density, temperature and magnetic field components in cgs units [g/cm^3, K and Gauss]. Each cell has a comoving size of 83.3 kpc. 
The data are written in HDF5 format (https://support.hdfgroup.org/HDF5/). 
We additionally provide also .fits maps of the X and Z projection across the box, showing the volume weighted mean density, DM density, temperature, |B| and Bz. 
For more details on the simulations please refer to 
http://cosmosimfrazza.myfreesites.net/magnetic-models
Vazza et al. 2017 CQG (http://iopscience.iop.org/article/10.1088/1361-6382/aa8e60) 
For parent models with primordial seeding models and non-radiative gas physics see https://b2share.eudat.eu/records/cf49996d869540b6aefc9a06ee5082f5
DOI: 10.23728/b2share.d647ba025b5144d79b8bcfd3bb8053c7
title: Simulated cosmic volume - dynamo amplification

description: This is one subset (300^3 cells) derived from a larger 1024^3 cosmological MHD simulation produced using ENZO on Piz-Daint (CSCS) by F.Vazza& collaborators. In these "dynamo" models we impose a negligibly small initial seed field, and allow for the small-scale dynamo amplification of magnetic fields, based on the amount of solenoidal turbulence measured at run-time. The run is non-radiative.
These dataset are extracted around a massive cluster at z=0, and give gas density, Dark Matter density, temperature and magnetic field components in cgs units [g/cm^3, K and Gauss]. Each cell has a comoving size of 83.3 kpc. The data are written in HDF5 format (https://support.hdfgroup.org/HDF5/). We additionally provide also .fits maps of the X and Z projection across the box, showing the volume weighted mean density, DM density, temperature, |B| and Bz. For more details on the simulations please refer to http://cosmosimfrazza.myfreesites.net/magnetic-models Vazza et al. 2017 CQG (http://iopscience.iop.org/article/10.1088/1361-6382/aa8e60) 
For parent models with primordial seeding models and non-radiative gas physics see https://b2share.eudat.eu/records/cf49996d869540b6aefc9a06ee5082f5
DOI: 10.23728/b2share.66b53b05ebe248d7a01efc3e2556752d
title: Air quality data from the LIFE+RESPIRA project in Pamplona, Spain: NO at 01h CET (dataset)

description: csv file including air quality data from the LIFE+RESPIRA project (http://www.liferespira.eu/) in Pamplona, Spain, with measures of nitrogen monoxide, aggregated by hour (01h CET).
DOI: 10.23728/b2share.c31bf28c4763457bafc8d6f2a3dcbe25
title: Air quality data from the LIFE+RESPIRA project in Pamplona, Spain: NO (01h CET) (shapefile)

description: Shapefile including air quality data from the LIFE+RESPIRA project (http://www.liferespira.eu/) in Pamplona, Spain, with measures of nitrogen monoxide, aggregated by hour (01h CET).
DOI: 10.23728/b2share.c0c432f5d3ff466b9ea0c1c0cf499fc7
title: 1-D beams crossing a perturbed simulated gal.cluster

description: 150 lines of sight through the volume of a simulated galaxy cluster at z=0, produced by F.Vazza et al. running ENZO-MHD on the Jureca supercluster in Juelich.
Each line is simple tabulated dataset containing
1st col=distance along axis (in comoving kpc)
2=gas density g/cm^3
3=temperature[K]
4,5,6 = Bx,By,Bz in microGauss
7,8 = position along x and y in cell units.
The beams are sweeping the cluster along the Z-direction. Each cell is 3.95 kpc and the centre of the cluster in this case is at 640,640.
The "random" dataset contain 100 beams at random x,y location in the projected cluster area, the "central" dataset contains 50 beams closely extracted around the cluster core. The cluster has a final mass of ~1e15Msol and the magnetic field model assumes an initial seed field of 0.1nG (comoving). More info in Vazza et al. 2017 MNRAS (forthcoming publication)
DOI: 10.23728/b2share.b2962aa4e8bd41bca5247b6b05bfaef5
title: Air quality data from the LIFE+RESPIRA project in Pamplona, Spain: NO (01h CET) (interpolated GeoTIFF)

description: GeoTIFF file including interpolated air quality data from the LIFE+RESPIRA project (http://www.liferespira.eu/) in Pamplona, Spain, with measures of nitrogen monoxide, aggregated by hour (01h CET).
DOI: 10.15468/dl.zejync
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lathyrus woronowii Bornm."
 ]
}

 The dataset includes 10 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042601-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.23728/b2share.7fafef0af6184182820b124a29948cb4
title: 1-D beams crossing a relaxed simulated gal.cluster

description: 150 lines of sight through the volume of a simulated relaxed galaxy cluster at z=0, produced by F.Vazza et al. running ENZO-MHD on the Jureca supercluster in Juelich. Each line is simple tabulated dataset containing 1st col=distance along axis (in comoving kpc) 2=gas density g/cm^3 3=temperature[K] 4,5,6 = Bx,By,Bz in microGauss 7,8 = position along x and y in cell units. The beams are sweeping the cluster along the Z-direction. Each cell is 3.95 kpc and the centre of the cluster in this case is at 640,640. The "random" dataset contain 100 beams at random x,y location in the projected cluster area, the "central" dataset contains 50 beams closely extracted around the cluster core. The cluster has a final mass of ~1e15Msol and the magnetic field model assumes an initial seed field of 0.1nG (comoving). More info in Vazza et al. 2017 MNRAS (forthcoming publication)
DOI: 10.15468/dl.byh8uy
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lepidagathis papuana S.Moore"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042600-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.23728/b2share.da7a9156dc0e451986ed358acb05ceb3
title: Air quality data from the LIFE+RESPIRA project in Pamplona, Spain: NO (01h CET) (interpolated PNG)

description: PNG image representing interpolated air quality data from the LIFE+RESPIRA project (http://www.liferespira.eu/) in Pamplona, Spain, with measures of nitrogen monoxide, aggregated by hour (01h CET).
DOI: 10.23728/b2share.9dcdddd89b52417080c5204198e68249
title: Air quality data from the LIFE+RESPIRA project in Pamplona, Spain: NO (01h CET) (clipped GeoTIFF)

description: Clipped GeoTIFF file including interpolated air quality data from the LIFE+RESPIRA project (http://www.liferespira.eu/) in Pamplona, Spain, with measures of nitrogen monoxide, aggregated by hour (01h CET).
DOI: 10.23728/b2share.e1349a793abd41cea0ceb6c6a5faa840
title: Air quality data from the LIFE+RESPIRA project in Pamplona, Spain: NO (01h CET) (clipped PNG)

description: PNG image representing clipped interpolated air quality data from the LIFE+RESPIRA project (http://www.liferespira.eu/) in Pamplona, Spain, with measures of nitrogen monoxide, aggregated by hour (01h CET).
DOI: 10.23728/b2share.ae8b9fed0ec04b0eb4a8cc78560f246d
title: Air quality data from the LIFE+RESPIRA project in Pamplona, Spain: O3 in 2015 (01h CET) (interpolated PNG)

description: PNG image representing interpolated air quality data from the LIFE+RESPIRA project (http://www.liferespira.eu/) in Pamplona, Spain, with measures of ozone during 2015, aggregated by hour (01h CET).
DOI: 10.23728/b2share.f3906a7d866c429585925ac2dc8d31ff
title: Air quality data from the LIFE+RESPIRA project in Pamplona, Spain: O3 at 01h CET (dataset)

description: csv file including air quality data from the LIFE+RESPIRA project (http://www.liferespira.eu/) in Pamplona, Spain, with measures of ozone, aggregated by hour (01h CET).
DOI: 10.23728/b2share.5ce2e547d3804367b2a8952de8d78347
title: Air quality data from the LIFE+RESPIRA project in Pamplona, Spain: O3 (01h CET) (shapefile)

description: Shapefile including air quality data from the LIFE+RESPIRA project (http://www.liferespira.eu/) in Pamplona, Spain, with measures of ozone, aggregated by hour (01h CET).
DOI: 10.23728/b2share.20ddec8d763841be8a43237be2fc44ac
title: Air quality data from the LIFE+RESPIRA project in Pamplona, Spain: O3 (14h CET) (interpolated GeoTIFF)

description: GeoTIFF file including interpolated air quality data from the LIFE+RESPIRA project (http://www.liferespira.eu/) in Pamplona, Spain, with measures of ozone, aggregated by hour (14h CET).
DOI: 10.15468/dl.pwtkg8
title: Occurrence Download

description: A dataset containing 76 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leptoderris miegei Aké Assi & Mangenot"
 ]
}

 The dataset includes 76 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042602-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.23728/b2share.b8e5fc40593745f580710f562b93e758
title: Air quality data from the LIFE+RESPIRA project in Pamplona, Spain: O3 (01h CET) (interpolated PNG)

description: PNG image representing interpolated air quality data from the LIFE+RESPIRA project (http://www.liferespira.eu/) in Pamplona, Spain, with measures of ozone, aggregated by hour (01h CET).
DOI: 10.23728/b2share.2420d1f708ea4455bab19c31eed742af
title: E14 high resolution dataset (innermost volume)

description: 3D dimensional dataset (256^3 cells) in HDF5 format, of a high-resolution MHD cosmological simulations obtained with the ENZO code (Bryan et al. 2015). The data are mapped onto the highest resolution level available (3.95 kpc) and the region is the innermost ~Mpc^3 of a relaxed 1e15Msol cluster at z=0. The fields included are: - gas density [code units], gas temperature [K] and dark matter density [code units]; - x/y/z component of magnetic field, in code units. For the conversion into cgs: - gas/dark matter density must be multiplied by 2.6666447e-30 to get them in g/cm^3 - B-field values must be multiplied by 3.74068e-05 to get them in Gauss. For more details, see http://cosmosimfrazza.myfreesites.net/amr-clusters Vazza et al. 2017 MNRAS (https://academic.oup.com/mnras/article-abstract/doi/10.1093/mnras/stx2830/4584474)
DOI: 10.23728/b2share.720bc2e826394cacb65ea2cde1652fc3
title: E18 cluster data at the 6th AMR level

description: 3D dimensional dataset (256^3 cells) in HDF5 format, of a high-resolution MHD cosmological simulations obtained with the ENZO code (Bryan et al. 2015), employing 6 levels of adaptive mesh refinement. The data are mapped onto the highest resolution level available (15.8 kpc) and the region is the innermost ~Mpc^3 of a perturbed 1e15Msol cluster at z=0. The fields included are: - gas density [code units], gas temperature [K] and dark matter density [code units]; - x/y/z component of magnetic field, in code units. For the conversion into cgs: - gas/dark matter density must be multiplied by 2.6666447e-30 to get them in g/cm^3 - B-field values must be multiplied by 3.74068e-05 to get them in Gauss. For more details, see http://cosmosimfrazza.myfreesites.net/amr-clusters Vazza et al. 2017 MNRAS (https://academic.oup.com/mnras/article-abstract/doi/10.1093/mnras/stx2830/4584474)
DOI: 10.23728/b2share.83793b19884d46899bb2f4ed69eca6c8
title: E18 cluster data at the 4th and 5th AMR levels

description: 3D dimensional dataset (256^3 cells) in HDF5 format, of a high-resolution MHD cosmological simulations obtained with the ENZO code (Bryan et al. 2015), employing 4 or 5 levels of adaptive mesh refinement. The data are mapped onto the highest resolution level available (31.6 or 63.2 kpc) and the region is the innermost region of a perturbed 1e15Msol cluster at z=0. 
The fields included are:
 - gas density [code units], gas temperature [K] and dark matter density [code units];
 - x/y/z component of magnetic field, in code units. 
- x/y/z component of the gas velocity in code units.
For the conversion into cgs: 
- gas/dark matter density must be multiplied by 2.6666447e-30 to get them in g/cm^3 
- B-field values must be multiplied by 3.74068e-05 to get them in Gauss. 
- velocity values must be multiplied by 6.4770872e09 to get them in cm/s.

For more details, see http://cosmosimfrazza.myfreesites.net/amr-clusters Vazza et al. 2017 MNRAS (https://academic.oup.com/mnras/article-abstract/doi/10.1093/mnras/stx2830/4584474)
DOI: 10.23728/b2share.6d6c6a53a0354a89aba92757d549f9c8
title: Air quality data from the LIFE+RESPIRA project in Pamplona, Spain: O3 (01h CET) (clipped GeoTIFF)

description: Clipped GeoTIFF file including interpolated air quality data from the LIFE+RESPIRA project (http://www.liferespira.eu/) in Pamplona, Spain, with measures of ozone, aggregated by hour (01h CET).
DOI: 10.23728/b2share.db2debebd0da4b73acf8c4e8d334b268
title: Cluster IT90_3 data at z=0

description: 3-D distribution of gas density, dark matter density, temperature, and 3-components of velocity field for cluster IT90_3 at z=0, simulated with the ENZO code (Bryan et al. 2015). The fixed resolution of these reconstructed data is 20kpc/cell.
The additional .conv2 file gives the additional useful quantities to convert from Enzo's internal units to cgs:

snapshot number

time (internal code units)

redshift

conversion factor to get density in g/cm^3

conversion factor to get velocity in cm/s

For more details, please refer to

- http://cosmosimfrazza.myfreesites.net/isc-project

-http://adsabs.harvard.edu/abs/2016arXiv160903558V

-http://adsabs.harvard.edu/abs/2017MNRAS.471.3212W
DOI: 10.15468/dl.n474rw
title: Occurrence Download

description: A dataset containing 5535 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ligustrum quihoui Carrière"
 ]
}

 The dataset includes 5535 records from 100 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042603-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.23728/b2share.150408ab323945d59f1f15730322dbc4
title: Air quality data from the LIFE+RESPIRA project in Pamplona, Spain: O3 in 2015 (01h CET) (clipped GeoTIFF)

description: Clipped GeoTIFF file including interpolated air quality data from the LIFE+RESPIRA project (http://www.liferespira.eu/) in Pamplona, Spain, with measures of ozone during 2015, aggregated by hour (01h CET).
DOI: 10.15468/dl.v8mn5b
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lithocarpus perakensis Soepadmo"
 ]
}

 The dataset includes 13 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042604-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.23728/b2share.d044a5002607483cb7208d4b935d83e0
title: Air quality data from the LIFE+RESPIRA project in Pamplona, Spain: O3 (01h CET) (clipped PNG)

description: PNG image representing clipped interpolated air quality data from the LIFE+RESPIRA project (http://www.liferespira.eu/) in Pamplona, Spain, with measures of ozone, aggregated by hour (01h CET).
DOI: 10.23728/b2share.cf0f2a6c20fe4091bb2de6945685a614
title: Air quality data from the LIFE+RESPIRA project in Pamplona, Spain: PM1, PM2.5 and PM10 at 01h CET (dataset)

description: csv file including air quality data from the LIFE+RESPIRA project (http://www.liferespira.eu/) in Pamplona, Spain, with measures of PM1, PM2.5 and PM10 particles, aggregated by hour (01h CET).
DOI: 10.23728/b2share.c4230941b52941bca170ace63dea390b
title: Cluster IT90_0 data at z=0

description: 3-D distribution of gas density, dark matter density, temperature, and 3-components of velocity field for cluster IT90_0 (relaxed) at z=0, simulated with the ENZO code (Bryan et al. 2015). The fixed resolution of these reconstructed data is 20kpc/cell. 

The additional .conv2 file gives the additional useful quantities to convert from Enzo's internal units to cgs: snapshot number time (internal code units) redshift conversion factor to get density in g/cm^3 conversion factor to get velocity in cm/s 

For more details, please refer to - http://cosmosimfrazza.myfreesites.net/isc-project -http://adsabs.harvard.edu/abs/2016arXiv160903558V -http://adsabs.harvard.edu/abs/2017MNRAS.471.3212W
DOI: 10.23728/b2share.e5536414ae6e41b0bc2ce9ba3bf61fa3
title: Air quality data from the LIFE+RESPIRA project in Pamplona, Spain: PM1, PM2.5 and PM10 (01h CET) (shapefile)

description: Shapefile including air quality data from the LIFE+RESPIRA project (http://www.liferespira.eu/) in Pamplona, Spain, with measures of PM1, PM2.5 and PM10 particles, aggregated by hour (01h CET).
DOI: 10.23728/b2share.79864af7bbc94fdcb884621abee31e57
title: Air quality data from the LIFE+RESPIRA project in Pamplona, Spain: O3 in 2015 (01h CET) (clipped PNG)

description: PNG image representing clipped interpolated air quality data from the LIFE+RESPIRA project (http://www.liferespira.eu/) in Pamplona, Spain, with measures of ozone during 2015, aggregated by hour (01h CET).