BOL: Related items

Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the recontruction, manipulation, analysis and visualization of phylogenetic trees

Rahul Nayak — Wed, 27 Nov 2019 05:32:33 -0600

The Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the recontruction, manipulation, analysis and visualization of phylogenetic trees (although clustering trees or any other tree-like data structure are also supported).

Other tools

https://github.com/shenwei356/taxonkit

ETE, version: 3.1.1
BioPython, version: 1.73
taxadb, version: 0.10.1
TaxonKit, version: 0.5.0

Address of the bookmark: https://pypi.org/project/ete3/3.1.1/

Flanker

Rahul Nayak — Sat, 27 Feb 2021 22:04:53 -0600

Flanker, a Python package which performs alignment-free clustering of gene flanking sequences in a consistent format, allowing investigation of mobile genetic elements (MGEs) without prior knowledge of their structure. Flanker can be flexibly parameterised to finetune outputs by characterising upstream and downstream regions separately and investigating variable lengths of flanking sequence.

Address of the bookmark: https://github.com/wtmatlock/flanker

Creating conda environment for python2.7

Jit — Mon, 07 May 2018 08:56:52 -0500

TIP: By default, environments are installed into the envs directory in your conda directory. Run conda create --help for information on specifying a different path.

Use the Terminal or an Anaconda Prompt for the following steps.

To create an environment:
```
conda create --name myenv
```
NOTE: Replace myenv with the environment name.
When conda asks you to proceed, type y:
```
proceed ([y]/n)?
```

This creates the myenv environment in /envs/. This environment uses the same version of Python that you are currently using, because you did not specify a version.

To create an environment with a specific version of Python:

conda create -n myenv python=3.4

To create an environment with a specific package:

conda create -n myenv scipy

OR:

conda create -n myenv python
conda install -n myenv scipy

To create an environment with a specific version of a package:

conda create -n myenv scipy=0.15.0

OR:

conda create -n myenv python
conda install -n myenv scipy=0.15.0

To create an environment with a specific version of Python and multiple packages:

conda create -n myenv python=3.4 scipy=0.15.0 astroid babel

TIP: Install all the programs that you want in this environment at the same time. Installing 1 program at a time can lead to dependency conflicts.

To automatically install pip or another program every time a new environment is created, add the default programs to the create_default_packages section of your .condarc configuration file. The default packages are installed every time you create a new environment. If you do not want the default packages installed in a particular environment, use the --no-default-packages flag:

conda create --no-default-packages -n myenv python

TIP: You can add much more to the conda create command. For details, run conda create --help.

➜ redundans git:(master) ✗ conda create --name py27 python=2.7
Solving environment: done

==> WARNING: A newer version of conda exists. <==
current version: 4.5.0
latest version: 4.5.2

Please update conda by running

$ conda update -n base conda

## Package Plan ##

environment location: /home/urbe/anaconda3/envs/py27

added / updated specs:
- python=2.7

The following packages will be downloaded:

package | build
---------------------------|-----------------
wheel-0.31.0 | py27_0 61 KB
python-2.7.15 | h1571d57_0 12.1 MB
certifi-2018.4.16 | py27_0 142 KB
sqlite-3.23.1 | he433501_0 1.5 MB
setuptools-39.1.0 | py27_0 582 KB
openssl-1.0.2o | h20670df_0 3.4 MB
pip-10.0.1 | py27_0 1.7 MB
ca-certificates-2018.03.07 | 0 124 KB
------------------------------------------------------------
Total: 19.6 MB

The following NEW packages will be INSTALLED:

ca-certificates: 2018.03.07-0
certifi: 2018.4.16-py27_0
libedit: 3.1-heed3624_0
libffi: 3.2.1-hd88cf55_4
libgcc-ng: 7.2.0-hdf63c60_3
libstdcxx-ng: 7.2.0-hdf63c60_3
ncurses: 6.0-h9df7e31_2
openssl: 1.0.2o-h20670df_0
pip: 10.0.1-py27_0
python: 2.7.15-h1571d57_0
readline: 7.0-ha6073c6_4
setuptools: 39.1.0-py27_0
sqlite: 3.23.1-he433501_0
tk: 8.6.7-hc745277_3
wheel: 0.31.0-py27_0
zlib: 1.2.11-ha838bed_2

Proceed ([y]/n)? y

Downloading and Extracting Packages
wheel 0.31.0: #################################################################################################################################################################################################### | 100%
python 2.7.15: ################################################################################################################################################################################################### | 100%
certifi 2018.4.16: ############################################################################################################################################################################################### | 100%
sqlite 3.23.1: ################################################################################################################################################################################################### | 100%
setuptools 39.1.0: ############################################################################################################################################################################################### | 100%
openssl 1.0.2o: ################################################################################################################################################################################################## | 100%
pip 10.0.1: ###################################################################################################################################################################################################### | 100%
ca-certificates 2018.03.07: ###################################################################################################################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use:
# > source activate py27
#
# To deactivate an active environment, use:
# > source deactivate
#

➜ redundans git:(master) ✗ source activate py27

Tools for Geospatial data analysis !

BioStar — Wed, 22 Mar 2023 02:10:28 -0500

Geospatial data is becoming increasingly important in many fields, including urban planning, environmental science, public health, and more. These tools can help you work with data from a variety of sources, including satellite imagery, GPS data, and other forms of spatial data. They can help you visualize data, perform complex analysis, and even create maps and other visualizations.

The list includes some of the most popular and widely used geospatial tools available in Python. These tools can help you work with data from a variety of sources and in a variety of formats. Some of the tools are focused on visualization, such as Cartopy, Folium, and Contextily, which allow you to create interactive maps and other visualizations. Other tools are more focused on data manipulation and analysis, such as Fiona, GeoPandas, and Rasterio, which allow you to manipulate and analyze spatial data in a variety of ways.

The list also includes some tools for working with specific types of geospatial data. For example, the H3 library is designed specifically for working with hexagonal grids, while PySAL is focused on spatial econometrics and spatial analysis. Whether you are a data scientist, GIS specialist, or geospatial enthusiast, these tools are sure to enhance your work and help you achieve your goals.

In summary, this list is an excellent resource for anyone working with geospatial data in Python. It contains a wide range of tools for working with different types of data, and can help you visualize data, perform complex analysis, and create maps and other visualizations. If you're looking to enhance your skills in geospatial analysis, this list is definitely worth checking out.

These tools are:

ArcGIS - https://lnkd.in/dgC6sKJH
Cartopy - https://lnkd.in/dc8ijXRg
Contextily - https://lnkd.in/dTdQsmKX
Descartes - https://lnkd.in/dCJykxwW
Fiona - https://lnkd.in/d8sJ3Q5a
Folium - https://lnkd.in/dfSsE-MB
GDAL - https://lnkd.in/dYBJBaAY
Geohash - https://lnkd.in/d_NxJ4_M
GeoJSON - https://lnkd.in/daGs2WYq
GeoPandas - https://lnkd.in/dBTFKKV3
Geopy - https://lnkd.in/dfAzR8Xa
Gevent - http://www.gevent.org
H3 - https://h3geo.org/docs/
OSMnx - https://lnkd.in/dm3pHgUS
PyQGIS - https://lnkd.in/dShWyWVr
PySAL - https://pysal.org
Pydeck - https://lnkd.in/dGBFu-iw
Pyproj - https://lnkd.in/dNG9fdkm
RTree - https://lnkd.in/dURMiYpU
Rasterio - https://lnkd.in/dEMC6ve6
Scikit-mobility - https://lnkd.in/dpHhaX2J
Shapely - https://lnkd.in/d568datK

These tools offer a wide range of capabilities for working with geospatial data, from visualizing and manipulating data to performing complex analysis and modeling. Whether you are a data scientist, GIS specialist, or geospatial enthusiast, these tools are sure to enhance your work and help you achieve your goals.

PostDoc Scientist Bioinformatics at CCMB

Fri, 26 Sep 2014 19:58:41 -0500

1. Project Assistant/Junior Research Fellow/ Project Fellow [PA_JRF_PF]

a) M.Sc/or equivalent in biological sciences/related areas [Position Code: PA_JRF_PF_a]
b) B.E/B.Tech/ M.Sc in biotechnology/bioinformatics/computer science/Chemistry/Physics or MCA [Position Code: PA_JRF_PF_b]
c) M.Sc/or equivalent in wildlife sciences/ecology/environmental sciences or MBBS/BVSc/MVSc. [Position Code: PA_JRF_PF_c]

(Candidates with result awaited are NOT eligible to apply)

Upper Age limit 28years

Rs.12000 / Rs.16000 (as sanctioned by the funding agency)

2. Post Doctoral Fellow/Research Associate in multiple research areas [PDF_RA]

Ph.D. (submitted/awarded) in any branch of biological Sciences. Candidates with Ph.D. in other sciences are also encouraged to apply.

Experience in molecular biology, biochemistry, structural biology, cell biology, infectious disease, conservation genetics, veterinary science, reproductive biology, and molecular diagnostics is desired but not mandatory.

[Position Code: PDF_RA]

UpperAge limit 35years

Rs. 22000- 26000 (as sanctioned by the funding agency)

3. Post Doctoral Scientist Fellow [PDSF]

Ph.D in any of the following areas: bioinformatics, next generation sequencing, high throughput data analysis, proteomics, bio-statistics, computer science, information technology, computer hardware and networking/clustering, parallel processing.
[Position Code: PDSF]

Upper Age limit 40 years

Rs. 40000 consolidated (as sanctioned by the funding agency)

Download Application: Last date for apply online: 09th Oct 2014

Advertisement: www.ccmb.res.in//index.php?view=notifications&mid=0&id=71&nid=38

Apply online http://www.ccmb.res.in/positions/temp_notif/online_form.html

More at http://www.ccmb.res.in//index.php?view=notifications&mid=0&id=71&nid=38

ArrayGen Bioinformatics Genomics Group

Sun, 28 Sep 2014 14:09:55 -0500

ArrayGen is a global bioinformatics company which is a one stop solution for microarray designing and genomics data analysis. Our novel Array Design Approach Strategy (ADAS) aims to condense the time lag between demands of scientific community and manufacture industry, thereby expediting research processes.

ArrayGen specializes in Genomics data analysis and research, as we believe in the level of precision, predictability, benchmark-ability, and data analysis capability of genomics data over other forms of biological data. ArrayGen constantly strives to develop new solutions, and plug the existing gaps in the technological advancement of the field.

More http://www.arraygen.com/

Postdoc position in protein annotation and machine learning - Paris, France

Sat, 04 Oct 2014 08:10:45 -0500

We are interested in finding an excellent postdoc with interests in protein functional annotation, machine learning and computer grids. The position is open for 3.5 years at the Université Pierre et Marie Curie, in the heart of Paris.

Research topic: Protein function annotation, multiple probabilistic models, domain architecture, machine learning, combinatorial optimization, computer grid.

This project is run on the Laboratoire de Biologie Computationnelle et Quantitative UMR7238 CNRS-UPMC – Analytical Genomics team, headed by A.Carbone. It is co-advised with Pierre-Henri Wuillemin, Laboratoire d’Informatique de Paris 6 – Equipe DECISION.

The postdoc will be payed under a contract of Ingénieur de Recherche lasting 3.5 years and it is available from September 1st, 2014.

Group Web Page: http://www.lcqb.upmc.fr/AnalGenom/home.html

Ref. E-Mail: Alessandra Carbone alessandra.carbone@lip6.fr

JRF/SRF at Jawaharlal Nehru Institute ofAdvanced Studies (JNIAS), Hyderabad

Fri, 31 Oct 2014 08:48:23 -0500

Applications for Academic Projects in Biotechnology, Bioinformatics, Environmental Sciences and Computer Science & Engineering

About JNIAS
Jawaharlal Nehru Institute of Advanced Studies (JNIAS), Hyderabad has been established by Dr. D. Swaminadhan Research Foundation (DSRF), Hyderabad as a Research and Educational Institution with a view to contribute in developing advanced technologies and build „core competence‟ in specific areas. The activities of JNIAS involves: Education, Research Training and Innovations in the fields of Sciences, Technologies, Humanities and Social Sciences. It aims to blossom into an Advanced Institute of education and research with a reservoir of expertise and experience in the relevant fields and the necessary capability to harness multi-disciplinary research and studies. JNIAS has been recognized as an Advanced Research Institute by Jawaharlal Nehru Technological University Hyderabad (JNTUH), Hyderabad and Jawaharlal Nehru Technological University Anantapur (JNTUA), for offering Ph.D., P.G M.Phil, P.G Diploma and Training Programmes in Sciences and Engineering & Technology.

Jawaharlal Nehru Architecture and Fine Arts University (JNAFAU) Hyderabad also recognized JNIAS for offering UG, PG degree in Architecture.

Projects & Facilities

JNIAS offers wide range of projects:

Biotechnology area:

Molecular Biology
Microbiology
Nanotechnology
Bioinformatics (Schrodinger Software)
In Silico studies & Drug Designing
Sequence analysis
Protein structure function studies

Registration
Tuition Fees: Interested students need to pay the following tuition fees:
1. Six Month’s Project: Rs. 20,000/-
2. Four Month’s Project: Rs. 15,000/-
3. Three Month’s Project: Rs. 10,000/-
4. One Month - Hands on Training : Rs. 8,000/-

For enquires call:
91-7893203414 (Biotechnology), 91-9949582263 (Environmental Sciences) 91-8977369305 (Computer Science)

Interested student may download the application from the website (www.jnias.in) and send the hard copy of the completed application forms and Curriculum Vitae along with the Demand Draft drawn on any nationalized Banks in favor of “The Registrar, JNIAS, Secunderabad”. Application forms can be sent through email to academicprojects@jnias.in

Address
Jawaharlal Nehru Institute of Advanced Studies (JNIAS)
6th Floor, Buddha Bhavan, M.G Road,
Secunderabad - 500 003
Andhra Pradesh, India
Tele/Fax: 040- 27541551; 27541553
Mobile: 08885541554
Web site: www.jnias.in

Brochure : https://drive.google.com/file/d/0B3zPwhgA-u-nU0dyMFd2OWcxNUpSTWNYc0xDSGs5UDI4UDNB/view?usp=sharing

Celebrating Crystallography - An animated adventure

Fri, 31 Oct 2014 15:59:00 -0500

NEW: Now with French or Spanish subtitles (click on the 'Captions' icon to select). Plus... Watch the French language version here: https://www.youtube.com/watch?v=PvLu7BOsJhM X-ray crystallography is arguably one of the greatest innovations of the twentieth century, but not that many people know what it is or how it came about. Join us on an animated journey through the 100 year history of crystallography -- from the pioneering work of William and Lawrence Bragg in 1913 to the surface of Mars! Narrated by structural biologist Stephen Curry and produced by animation company 12foot6, the film explores the extraordinary history of crystallography. To date 28 Nobel Prizes have been awarded to projects related to the field and X-ray crystallography remains the foremost technique in determining the structures of a huge range of complex molecules. This film was produced in celebration of the Bragg Centenary and was funded by STFC. Watch more science videos on the amazing Ri Channel: http://richannel.org Watch more animations from 12foot6: http://12foot6.com/ The Ri is on Twitter: http://twitter.com/ri_science and Facebook: http://www.facebook.com/royalinstitution Subscribe for the latest science videos: http://richannel.org/newsletter

Centre for Systems Biology & Bioinformatics, Panjab University vacancy of Research Fellow

Wed, 12 Nov 2014 06:18:54 -0600

Applications are invited along with complete bio-data and attested copies of certificates of qualifications, experience etc. for the one post of
Research Fellow and one post of Program Assistant under PURSE Grant of the University in Centre for Systems Biology & Bioinformatics, UIEAST, Panjab University, Chandigarh which is tenable till the period of the project

Essential Qualification
For Research Fellow:-
M.Sc. in Systems Biology and Bioinformatics / Life
Sciences with minimum 55% marks.
Preference will be given to NET/GATE/ICMR qualified candidates without fellowship however, candidates who have cleared the Panjab University Ph.D. entrance test in Systems Biology & Bioinformatics will also be eligible.

Applications should be reach on or before 19-11-2014 in the office of the undersigned. Interview will be held on 21-11-2014 in the office of the Coordinator, Centre for Systems Biology & Bioinformatics, South Campus, Block-3, Sector-25, Panjab University, Chandigarh. No TA/DA will be paid.

more at http://jobs.puchd.ac.in/includes/jobs/2014/20141110143634-Advertisement.pdf