BOL: Related items

pipesnake: bioinformatics best-practice analysis pipeline for phylogenomic reconstruction

LEGE — Wed, 21 Feb 2024 06:19:41 -0600

ausarg/pipesnake is a bioinformatics best-practice analysis pipeline for phylogenomic reconstruction starting from short-read 'second-generation' sequencing data.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies.

Address of the bookmark: https://github.com/AusARG/pipesnake

Bioinformatics: The Bridge Between Curiosity and Discovery

BioStar — Mon, 24 Nov 2025 05:16:49 -0600

In the sprawling universe of modern science, bioinformatics stands as one of the most transformative and empowering fields of our time. It is where biology meets computation, where data becomes meaning, and where curiosity becomes discovery. If you’ve stepped into this world—or are considering it—here’s your reminder: you’re part of a revolution.

Why Bioinformatics Matters More Than Ever

Every day, our world generates massive amounts of biological data—from genome sequences to microbiome profiles to real-time pathogen surveillance. Hidden within these datasets are the answers to some of the greatest challenges humanity faces: emerging diseases, antimicrobial resistance, environmental stress, genetic disorders, sustainable agriculture, and more.

Bioinformatics isn’t just a skill.
It’s the language of the future of biology.

By mastering it, you give yourself the power to:

Decode genomes and understand life at its most fundamental level

Identify patterns no microscope could ever reveal

Predict disease outbreaks before they occur

Accelerate drug discovery with computational precision

Contribute to open-source tools that empower scientists worldwide

You don’t just follow science—you drive it.

Every Expert Was Once a Beginner

Many newcomers feel intimidated. Command-line interfaces. R scripts. Python packages. Next-generation sequencing data. Complex machine learning models.

But here’s the truth: every bioinformatician started exactly where you are now—curious, unsure, but excited.

No one writes perfect code on day one.

No one understands genomics pipelines immediately.

What makes you a bioinformatician is not perfection, but perseverance.

When your script throws a cryptic error…
When your data refuses to format…
When your pipeline runs for 6 hours only to crash…

Remember: this is part of the journey.
Every error teaches you. Every retry strengthens you. Every breakthrough energizes you.

Bioinformatics Is Not Just a Career—It’s a Mindset

It’s the mindset of:

Problem-solving.

Continuous learning.

Turning chaos into clarity.

Seeing what others can’t.

Bioinformaticians are detectives of biological complexity. You sit at the intersection of innovation, using tools that can shape public health, medicine, agriculture, and ecology. Few fields give you such direct impact on the world.

Your Contribution Matters

As you work on your script, pipeline, genome, or model, remember:

Somewhere, your analysis might contribute to:

A new therapy

A faster diagnostic test

A better understanding of a pathogen

A more resilient crop

An open-source dataset that helps thousands

A discovery that rewrites textbooks

Your code may be small, but its ripple effect is powerful.

The Future Is Bioinformatics—And You Are Part of It

The world is shifting. Wet labs are integrating AI. Hospitals rely on genomic insights. Farmers use gene-level predictions. Governments monitor disease in real time. Students launch pipelines that become global tools.

This is a golden era—and you are not late.
You are exactly where you need to be.

Keep Pushing. Keep Learning. Keep Discovering.

Bioinformatics is a journey filled with challenges, but also with unmatched rewards.

So the next time you feel stuck, frustrated, or overwhelmed, remember:
You’re building the science of tomorrow.

Be proud. Stay curious. Keep going.
Your work matters more than you think.

Nataša Pržulj Lab

Fri, 30 Aug 2013 06:29:17 -0500

Nataša Pržulj Lab's research involves applications of graph theory, mathematical modeling, and computational techniques to solving large-scale problems in computational and systems biology.They are interested in computational and theoretical solutions to practical problems in many areas of systems biology, planar cell polarity, proteomics, cancer informatics, and drug discovery and design.

More at http://www.doc.ic.ac.uk/~natasha/index.html

RA Bioinformatics at NII

Thu, 22 Oct 2015 01:56:26 -0500

NATIONAL INSTITUTE OF IMMUNOLOGY

NEW DELHI-110067

Applications are invited for the position of Research Associate (RA) for the following time-bound sponsored project as per the details given below:

1. BTIS project entitled, “National Infrastructural Facility in the Area of Immunology” funded by DBT

Research Associate (One Position only)

Dr. Debasisa Mohanty Staff Scientist-VI deb@nii.res.in

Educational Qualifications: Ph.D in Bioinformatics or Biological Sciences or Biotechnology with research experience and publication record in indexed peer reviewed journals in the area of bioinformatics or computational biology.

Emoluments: The selected candidates will draw consolidated emoluments as per Institute Rules, depending upon qualifications & experience Research Associate: Rs. 36,000/- per month plus 30% HRA

Job description & Desired Knowledge: The candidate should be well versed in Programming in PERL/C++, HTML, CGI, web sever and portal development, computational analysis of protein structure & function, molecular dynamics simulations and use of high performance computing systems.

General Terms & Conditions:-

1. The candidates selected for the above posts will be on contract for one year or duration of the project whichever is shorter, at a time.

2. No hostel/ housing facility will be provided.

3. Applicants may clearly mention the category they belong to i.e. SC/ST/OBC/PH and attach documentary proof of the same.

4. No TA/DA will be paid for attending the interview, if called for.

5. Apart from sending application in the prescribed format given below, candidates should send complete Curriculum Vitae along with the names of three referees. Curriculum Vitae should contain details of the experimental expertise and list of publications. 6. Canvassing in any form will be a disqualification.

HOW TO APPLY Interested candidates may apply directly, STRICTLY IN THE PRESCRIBED FORMAT GIVEN BELOW, through e-mail, to the Investigator of the project, clearly indicating the name of the project along with their complete C.V., Email ID, fax numbers, telephone numbers. Only Short listed candidates will be called for interview and they required to submit attested copies of all their certificates and a Demand Draft of Rs 100/- drawn on Canara Bank or Indian Bank payable at Delhi/New Delhi in favour of the Director, NII (SC/ST/PH and Women candidates are exempted from payment of fees) subject to submission of documentary proof), at the time of interview. (E-MAIL APPLICATIONS SHOULD MENTION BTIS-RA 2015 IN THE SUBJECT LINE)

LAST DATE OF RECEIPT OF APPLICATIONS: 29th October, 2015

www1.nii.res.in/sites/default/files/projectappointments-Dr.Mohanty-29oct2015.pdf

'What is Life? A 21st Century Perspective' by Dr Craig Venter

Mon, 26 Aug 2013 17:09:17 -0500

One of the landmark events of 20th century science was celebrated and reinterpreted for the 21st century in Trinity College Dublin on 12 July 2012 as part of the Science in the City programme of ESOF2012. Dr Craig Venter, one of the leaders of the Human Genome Project in the 1990s and a pioneer of synthetic biology delivered a lecture entitled, 'What is Life? A 21st century perspective' recreating the Irish event that inspired the discovery of the structure of DNA. In February, 1943 one of the most distinguished scientists of the 20th Century, Erwin Schrödinger, delivered a seminal lecture, entitled 'What is Life?', under the auspices of the Dublin Institute for Advanced Studies, in Trinity College Dublin. The lecture presented far-sighted ideas on how hereditary information could be encoded in a chemical structure (aperiodic crystal) in living cells. Schrödinger's book (1944) of the same title is considered to be a scientific classic. The book was cited by Crick and Watson as one of the inspirations which ultimately led them to unravel the structure of DNA in 1953, a breakthrough which won them the Nobel prize.

R Shiny in Life Sciences – Top 7 Dashboard Examples

Neel — Fri, 01 Apr 2022 19:05:03 -0500

R Shiny is one of the easiest ways for developers to make production-ready dashboards when speed and functionality are crucial. Shiny is approachable with a lot of documentation available, and because of this, a lot of developers/researchers with non-coding backgrounds are able to produce some impressive results. The whole ecosystem is easy to get your head around and pretty much limitless with regard to what you can do.

Address of the bookmark: https://www.r-bloggers.com/2022/03/r-shiny-in-life-sciences-top-7-dashboard-examples/

Understand Social Media Importance for Researchers With Benefits to the Strategy !

Rahul Nayak — Tue, 14 Jan 2020 23:21:11 -0600

Why have so many researchers embraced Facebook or Instagram pages? They understand the importance of social media and how it adds value. Now that consumers often experience interactions with companies that are not face-to-face, shifting to social media has become an ideal way to actively engage with researchers.

With social media, you have the opportunity to highlight all the best aspects of your research with one click. What information would be most useful for your potential and current research lab to have easy access to?

Don’t leave this vital question unanswered! Social media’s importance is seen when you realize your social pages become a hub for users to easily find out more about your research and what you care about, without clicking away from the app or website they’re already browsing.

You can use social media as a platform to distinguish your research from competing labs, too. Showing researchers that your research personality is clearly defined and consistent is valuable, but you also want to make sure you are also wrapping your research identity in with common trends on the internet (as appropriate) to show your alike researchers that you are up-to-date on the world around you.

Remember, you don’t want to sound inauthentic! Understanding the importance of social media and investing in it gives you the ability to show that you can connect on a personal level with your alike researchers.

The importance of social media is seen in that it provides value while also creating a low-cost way to market your research. Plus, social media allows you to have direct control over the messages you share with the world.

Although increasing and maintaining your presence effectively on social media is important, it is essential to be realistic about the amount of energy and time you might need to invest in reaching larger audiences.

These days, if you don’t have an online presence it affects which opportunities will come your way. I showed an example of someone looking for ECR conference speakers on Twitter and all suggestions in response to this were for ECRs who were on Twitter.

When someone Googles your name, what do they get? What do you want them to see? I gave my opinion on some profiles:

Google Scholar – essential. Sign up, and once you have a publication, make your profile public. Website – essential. As a minimum we add each person to the lab website with links to their professional profiles.
ORCiD – required. All lab members need an ORCiD for our publications. Easy to set up a profile and link to services that will auto-update it for you, e.g. when you publish a paper.
Twitter – important. Possibly essential these days. Many scientists are on Twitter and there are a lot of benefits to joining. It is somehow more professional than other social networks. Twitter handles can even be included on papers. Great for networking with other scientists and for following meetings. This a great guide to getting started.
LinkedIn – important outside of academia. I personally dislike LinkedIn, but it is essential if you are job-hunting outside of academic circles.
ImpactStory – not essential but fun. You can make a profile based on your ORCiD. It’s a good way to keep track of the attention that your work gets online.
Publons – might become important. This is a way to log your review activity.

Many places to set up an author profile, e.g. researcherid. Most are not worth bothering with if you have ORCiD and/or Google Scholar page.

ResearchGate – not important. It’s incredibly popular but I have never needed it and dislike it for similar reasons to LinkedIn.

How active you are on these platforms determines what you will get out of them, but as a minimum, try and keep them active and up-to-date.

I left it to the people in the lab to setup whatever accounts they like. A possibility is to get people to sign up right there in the session, but I think it’s important for everyone to make a choice about what profile(s) they want to create. The only one I require people in the lab to setup is ORCiD.

Internship program with ArrayGen Technolgies

Sun, 22 Jun 2014 23:18:31 -0500

Internship Program for Bioinformatics / Biotechnology Professionals Currently we offer positions to outstanding students interested in Next Generation Sequencing (NGS) data analysis. Applications are accepted throughout the year. Accepted students will be listed on web with their schedules. Accepted students can attend our future workshops and trainings freely at the specified venue.

Interested candidates may email their resume along with a cover letter to careers@arraygen.com

Official website: http://www.arraygen.com/

The 8000 years old Tibetian gene mutation !!!

Neel — Wed, 20 Aug 2014 21:57:44 -0500

A new study has provided insight into how gene mutation around 8,000 years ago helped Tibetans' to survive in the thin air on the Tibetan Plateau, where an average elevation is of 14,800 feet.

A study led by University of Utah scientists is the first to find a genetic cause for the adaptation, a single DNA base pair change that dates back 8,000 years and demonstrate how it contributes to the Tibetans' ability to live in low oxygen conditions.

About 8,000 years ago, the gene EGLN1 changed by a single DNA base pair. Today, a relatively short time later on the scale of human history, 88 percent of Tibetans have the genetic variation, and it was virtually absent from closely related lowland Asians. The findings indicate the genetic variation endows its carriers with an advantage.

In those without the adaptation, low oxygen caused their blood to become thick with oxygen-carrying red blood cells, an attempt to feed starved tissues, which could cause long-term complications such as heart failure. The researchers found that the newly identified genetic variation protected Tibetans by decreasing the over-response to low oxygen.

Reference: http://www.nature.com/nature/journal/v512/n7513/abs/nature13408.html

GrapheR !!!

John Parker — Thu, 14 Aug 2014 14:02:17 -0500

What a wonderful gem GrapheR is.... Oh yes it is. GrapheR is a GUI for base graphics in R by http://www.maximeherve.com/. The package provides a graphical user interface for creating base charts in R. It is ideal for beginners in R, as the user interface is very clear and the code is written along side into a text file, allowing users to recreate the charts directly in the console.

Adding and changing legends? Messing around with the plotting window settings? It is much easier/quicker with this GUI than reading the help file and trying to understand the various parameters.
Here is a little example using the iris data set.

library(GrapheR)
data(iris)
run.GrapheR()

This will bring up a window that helps me to create the chart and tweak the various parameters.

Finally, I find the underlying R code in a file created by GrapheR. For more details read also the package vignette, which is available in English, French and German!