BOL: Related items

Bioinformatics Training Collections !

BioStar — Sun, 05 Mar 2023 23:01:26 -0600

Useful list of bioinformatics training collections @ https://github.com/sib-swiss/training-collection

Address of the bookmark: https://github.com/sib-swiss/training-collection

Bioinformatics Opening at NIBMG, India

Sun, 03 Dec 2023 00:16:59 -0600

NIBMG is looking for motivated and bright individuals interested to explore career
opportunities for the position of Research Associate (Project Linked Person) for extramural
project funded by ICMR as per details given below.
Project Name: Fast detection of driver mutations and genes from cancer genomics data using
an integrative machine learning-based approach.

More at https://www.nibmg.ac.in/uploads/3c5d4da3fb31bef490a218805408c858.pdf

2013 NextGen Genomics & Bioinformatics Technologies (NGBT) Conference, New Delhi, INDIA

Thu, 08 Aug 2013 16:21:16 -0500

2013 NextGen Genomics & Bioinformatics Technologies (NGBT) Conference

SciGenom Research Foundation (SGRF) and Institute of Genomics and Integrative Biology (IGIB) are pleased to host the Next-Generation Sequencing and Bioinformatics for Genomics & Healthcare conference.

In the ten years since the first human reference genome was completed for US$3 billion the sequencing technologies have radically changed leading to great reduction in sequencing cost. Today a human genome can be sequenced for under US$ 5000 in less than two weeks. It is expected that by the end of 2015 the cost of sequencing a human genome will drop to below thousand dollars. The next generation sequencing technologies over the past five years have enabled a large number of genomic studies that impact human health and disease. Also, this has made possible the growth of microbial, animal and plant genomics studies. While the data production has increased at a rapid pace challenges remain in analyzing and understanding the data. The conference will cover the next generation sequencing (NGS) technologies, bioinformatics for NGS and applications of NGS in many areas including personalized medicine.

For more info : http://www.scigenomconferences.com/2013/default.php

Postdoc at UBasel Comparative Single Cell Genomics

Fri, 13 Dec 2024 12:46:19 -0600

A fully funded 4-year Postdoc position is available in the lab of Patrick
Tschopp at the University of Basel, Switzerland, study the molecular and
tissue-scale dynamics during the embryonic formation of the vertebrate
skeleton and compare it across different vertebrate species with distinct
habitats.

We are looking for a highly motivated candidate with a PhD degree in
Bioinformatics or a related field. Candidates are expected to have a
strong background in evolutionary biology and/or comparative functional
genomics. Additional experiences in single cell functional genomics
analyses, statistics and computational data analyses are a plus, as is
an interest in comparative developmental (EvoDevo) questions.

We offer a dynamic and interactive research environment with state-of-the
art research facilities, good research funding and internationally
competitive salaries.

The Tschopp lab (www.evolution.unibas.ch/tschopp/research/)
studies the gene regulatory mechanisms of cell type
specification and evolution in vertebrates. See also our
preprints at https://doi.org/10.1101/2024.03.26.586769 and
https://doi.org/10.1101/2024.11.28.625862 Applications should include
a motivation letter, a CV, a list of publications, a statement about
research interests, as well as the names and contact details of at
least two referees. Applications (in the form of a single .pdf file)
should be sent to Patrick Tschopp (patrick.tschopp@unibas.ch); review
of applications will begin on January 1st 2025, and will continue until
the position is filled.

Postdoctoral Associate - Bioinformatics at Duke University Medical Center

Sat, 10 Aug 2013 18:38:38 -0500

The Department of Biostatistics and Bioinformatics at Duke University Medical Center is seeking a Postdoctoral Associate for a one year appointment to work on several high-dimensional research projects. The specific goals of the project are to identify genes or molecular markers that are predictive of clinical outcomes in renal and prostate cancer.

Candidates must have: a PhD degree in statistics, biostatistics or bioinformatics, extensive experience in analyzing high-dimensional data (microarray, SNP, CNVs) and of validation approaches. In addition, experience in penalized regression methods, data base manipulation; and strong programming skills in order to conduct Monte Carlo studies and applications (R). Candidate must have excellent communication skills (verbal, written and presentation), a strong proficiency in Linux system.

This position is available immediately and will be filled as soon as possible. Appointment could be extended beyond the first year based on additional funding.

For more information about the Department of Biostatistics and Bioinformatics, please visit our website: http://www.biostat.duke.edu.

For more info: http://biostat.duke.edu/sites/biostat.duke.edu/files/Halabi%20-%20Postdoc%20Job%20Posting%202013%20updated.pdf

Duke University is an Equal Opportunity/Affirmative Action Employer.

Exploring Bioinformatics Job Websites: Your Gateway to a Thriving Career

BioStar — Sat, 19 Oct 2024 13:43:06 -0500

Bioinformatics is a rapidly growing field at the intersection of biology, computer science, and data analytics, with applications in healthcare, genomics, drug discovery, and more. As demand increases for skilled professionals who can manage, analyze, and interpret biological data, finding the right job opportunities can be challenging. Fortunately, numerous online platforms cater specifically to bioinformatics professionals, from academia to industry positions.

Here’s a curated list of the top websites offering bioinformatics job opportunities and postdoctoral fellowships worldwide.

1. General Bioinformatics Job Portals

These platforms are ideal for bioinformaticians seeking jobs in diverse sectors:

Nature Careers: A trusted resource for job seekers in the sciences, Nature Careers offers bioinformatics roles globally. Their specialized search function allows you to filter jobs by keyword, location, and more.
- Explore Bioinformatics Jobs on Nature Careers
Science Careers: A job board from the AAAS, this site focuses on STEM jobs, including numerous bioinformatics opportunities in academia and industry.
Euraxess: Euraxess is the go-to platform for researchers looking for jobs, fellowships, and funding across Europe and beyond. It lists both bioinformatics roles and research grants.
- Search Bioinformatics Jobs on Euraxess
ResearchGate Jobs: ResearchGate is widely known as a platform for researchers to share publications, but it also has a robust job board featuring bioinformatics positions globally.
FindAPostDoc: This site is dedicated to helping postdoctoral researchers find positions, with bioinformatics being a popular category.
Academic Positions: Targeting academic roles worldwide, Academic Positions lists bioinformatics jobs at universities and research institutions.
PostdocJobs.com: Specializing in postdoctoral roles, this platform is a great resource for early-career researchers looking for bioinformatics-related positions.
Scholarship Positions: In addition to jobs, Scholarship Positions provides information on scholarships, fellowships, and grants related to bioinformatics.

2. Fellowship and Training Opportunities in Bioinformatics

For those seeking fellowships or specialized training, these organizations offer postdoctoral programs, grants, and research opportunities:

NIH Office of Intramural Training and Education: The National Institutes of Health offer extensive research training programs for postdocs, including those in bioinformatics.
NSF Research Opportunity Awards: The National Science Foundation funds bioinformatics research at predominantly undergraduate institutions, providing fellowships and grants.
Top U.S. Universities: Many prestigious U.S. institutions, including Harvard, Berkeley, Yale, MIT, Johns Hopkins, UCSD, and Cornell, offer postdoctoral opportunities in bioinformatics.

3. Country-Specific Job and Fellowship Resources

If you're targeting a specific region, these platforms offer bioinformatics opportunities tailored to their respective countries:

Canada

CAPS/ACPP: The Canadian Association of Postdoctoral Scholars provides a job board, including bioinformatics roles in academia.
Banting Postdoctoral Fellowships: A prestigious fellowship program for postdocs in bioinformatics and related fields.
Mitacs Elevate: A Canadian initiative offering fellowships to connect postdoctoral researchers with industry partners.

United Kingdom

UKRI: The UK Research and Innovation body funds bioinformatics research and offers various grants.
The Royal Society: Provides funding schemes for researchers in bioinformatics.
Marie Skłodowska-Curie Actions: The MSCA funds fellowships and doctoral programs across Europe, including bioinformatics-related projects.
Wellcome Trust: Offers research funding and career development opportunities in health-related fields, including bioinformatics.

Europe

EMBO Fellowships: The European Molecular Biology Organization supports bioinformaticians through fellowships and career grants.
Max Planck Society: A leading research organization offering bioinformatics positions and fellowships across Europe.
Helmholtz Association: A major research organization in Germany offering bioinformatics roles in various disciplines.
Leibniz Association: Offers research opportunities, including bioinformatics, across its numerous institutes.

Australia and New Zealand

Australian Research Council: Offers funding and research schemes, including in bioinformatics.
Top Universities: Universities like Sydney, Melbourne, and Queensland have research programs in bioinformatics.

Asia

Japan Society for the Promotion of Science (JSPS): Offers fellowships for international researchers in bioinformatics.
Top Institutions: Universities like NUS, CAS, and IISc are leading hubs for bioinformatics research.

Middle East

Qatar Research, Development, and Innovation (QRDI): Offers research opportunities in bioinformatics.
KAUST: A leading university in Saudi Arabia offering bioinformatics research positions.

Africa

African Academy of Sciences: Provides career opportunities and research funding in bioinformatics across Africa.

Conclusion

The field of bioinformatics is full of exciting opportunities for those with the right skills. Whether you are looking for a postdoc position, research funding, or a long-term job in industry, these platforms are an excellent starting point. Explore, apply, and take the next step in your bioinformatics career!

Cracking the Code: A Guide to Bioinformatics Job Hunting

Abhi — Mon, 23 Dec 2024 19:36:41 -0600

Entering the world of bioinformatics is an exciting journey, filled with opportunities to combine biology, data science, and technology to address some of the most pressing scientific challenges. However, securing a position in this competitive field can be daunting, especially for newcomers. Here’s a guide to help you navigate the job-hunting process and land your dream role in bioinformatics.

1. Understand the Landscape

Before diving into applications, take the time to understand the bioinformatics job market. Common roles include:

Bioinformatics Analyst/Scientist: Focused on data analysis and interpretation.
Computational Biologist: Combines computational techniques with biological research.
Data Scientist in Genomics: Applies machine learning and statistical models to genomic data.
Software Developer in Bioinformatics: Designs and develops tools and pipelines for biological research.

Familiarize yourself with the key industries hiring bioinformaticians, such as academia, biotech, pharmaceuticals, healthcare, and agriculture.

2. Build a Strong Foundation

Bioinformatics demands a diverse skill set. Ensure you have a solid foundation in the following areas:

Programming Skills: Proficiency in Python, R, or Perl is often required. Familiarity with tools like Bash scripting and version control systems (e.g., Git) is a plus.
Statistics and Data Analysis: Knowledge of statistical methods, machine learning, and data visualization is crucial.
Biological Knowledge: Understanding genomics, transcriptomics, and proteomics will help you communicate effectively with biologists.
Specialized Tools and Databases: Be comfortable using tools like BLAST, Bowtie, and databases like NCBI and Ensembl.

3. Create a Winning Resume and Portfolio

Highlight your technical skills, biological knowledge, and relevant experience. Tips for a standout application:

Tailor your resume to each job, emphasizing skills mentioned in the job description.
Showcase your experience with real-world datasets by linking to your GitHub profile or online portfolio.
Include details of any publications, presentations, or significant projects.

4. Network Actively

Networking is often the key to discovering opportunities. Here’s how to build connections:

Attend Conferences and Workshops: Events like ISMB or specialized bioinformatics workshops are great for meeting professionals.
Engage Online: Join LinkedIn groups, participate in bioinformatics forums, and follow relevant hashtags on Twitter.
Leverage Alumni Networks: Connect with alumni from your university who are working in the field.

5. Gain Relevant Experience

Experience is a major factor for hiring managers. Ways to enhance your profile include:

Internships: Seek out internships in research labs or biotech companies.
Collaborations: Volunteer to work on projects with professors or peers.
Open Source Contributions: Participate in bioinformatics software development on platforms like GitHub.

6. Prepare for Interviews

Bioinformatics interviews often combine technical and behavioral questions. Prepare by:

Reviewing Key Concepts: Refresh your knowledge of algorithms, sequence analysis, and statistical methods.
Practicing Coding: Be ready to solve coding challenges or discuss code snippets.
Understanding the Organization: Research their recent projects, publications, or products.
Preparing Questions: Demonstrate interest by asking about their tools, workflows, or team structure.

7. Stay Resilient and Persistent

Job hunting can be a long process, but persistence pays off. Tips to keep moving forward:

Keep improving your skills by taking online courses or certifications.
Stay updated with advancements in bioinformatics by following journals and blogs.
Apply to multiple positions and don’t get discouraged by rejections. Each application is a learning experience.

Closing Thoughts

Landing a bioinformatics job requires a mix of technical expertise, networking, and resilience. By understanding the market, showcasing your skills effectively, and continuously learning, you’ll be well on your way to a rewarding career in this dynamic field. Remember, the key to cracking the code is perseverance—stay curious, stay determined, and success will follow.

A Bioinformatician’s Lament

LEGE — Thu, 29 May 2025 01:33:31 -0500

"I have a presentation tomorrow," they say,

With hopeful eyes, like it’s all child's play.
As if results bloom overnight, full-grown—
Not wrangled from chaos, and error-prone.

Oh brave soul, sit, let’s walk through the tale,
Of pipelines broken and servers that fail.
The journey starts: “The data? It’s there—
Just fetch it from S3, easy, I swear.”

Now I summon awscli with dread,
Reset my keys, credentials fed.
Configure regions, IAM roles too—
All this, and still no peek at the view.

Next up, the tool: “It’s open source!”
On GitHub, rotting, no sign of remorse.
Python 2.7, some GCC trick—
The install alone might make you sick.

Finally, progress! The pipeline runs…
Till RAM collapses and error stuns.
Oh, and the metadata? A crime,
Merged cells, font soup, out of time.

Sample IDs—what a cryptic game:
Sample_1, S1, sample-1... the same?
Controls mislabeled, cases flipped,
No wonder my sanity's starting to slip.

Then QC plots, PCA joy—
Wait, that’s a tumor labeled as a boy?
Clusters cross, and axes lie,
And I still don’t know which sample’s "guy."

But the clock ticks on, and it’s half-past doom,
They want the final UMAP soon.
With pastel colors, labeled clear—
"Can we move that legend to right here?"

Tweak by tweak, I adjust each frame,
Resize Panel B, annotate a name.
Export the plot—it starts to gleam…
Then my laptop crashes. I scream.

This is the grind, the long-haul game,
Where science hides behind code and flame.
No “Export to Nature” button to press,
Just toil and logic and hope for success.

So next time you whisper that fated line—
“I have a talk, can you make it shine?”
Know: bioinformatics is craft, not a click,
It’s science with scars, not just a quick fix.

To all who debug at 3AM light,
Who ghostwrite figures through sleepless night—
You are the backbone, silent and true,
First-author-worthy, if only they knew.

"कल मेरी प्रेज़ेंटेशन है," वो कहते हैं,

आशा भरी आँखों से, जैसे सब सहज है।
जैसे परिणाम रातोंरात प्रकट हो जाएं—
ना कि डेटा की भूलभुलैया से उखाड़े जाएं।

आओ बैठो, एक किस्सा सुनाता हूँ,
जहाँ पाइपलाइन टूटती है, और सर्वर भी थक जाते हैं।
कहानी शुरू होती है: “डेटा तो है—
बस S3 बकेट में, एकदम पास में कहीं।”

अब awscli बुलाता हूँ डरते हुए,
कुंजी सेट करूँ, क्रेडेंशियल जोड़ूं, रीजन भरूँ।
इतनी मशक्कत, फिर भी डेटा नहीं मिला,
बस सेटअप में ही पूरा दिन चला।

फिर आता है टूल: “ओपन-सोर्स है!”
GitHub पर है, 2019 से सूखा पड़ा है।
Python 2.7 चाहिए, एक पुराना कम्पाइलर,
और साथ में थोड़ी सी दुआ की ताकत।

आख़िरकार टूल चला, खुशी सी हुई,
लेकिन रन करते ही, मेमोरी ने हार मानी।
और मेटाडेटा? एक एक्सेल की आफ़त,
मर्ज़ किए हुए सेल, बस और क्या चाहिए काफ़ियत?

सैंपल आईडी? बस भगवान ही जाने—
Sample_1, sample-1, S1, और control1—
ये सब एक ही सैंपल हैं क्या?
पता तब चलता है जब पूछो दो-तीन बार।

काउंट मैट्रिक्स तैयार, अब R या Python की बारी,
QC करो, PCA प्लॉट—पर कुछ गड़बड़ भारी।
ट्यूमर और नॉर्मल का अदला-बदली खेल,
बार-बार, वही पुरानी झमेल।

आख़िर में आया मॉडलिंग का समय,
स्टैट्स, प्लॉट्स, डिफरेंशियल एक्सप्रेशन का श्रम।
लेकिन घड़ी में 5 बज चुके हैं जनाब,
और 8 बजे तक UMAP चाहिए, साफ़-सुथरा जबाब।

तो मैं कोड लिखता हूँ रात भर बैठ कर,
कलर पैलेट, जीन लेबल, लीजेंड बाहर रख कर।
फ़ॉन्ट, पैनल, एक्सिस सब सुधार,
एक्सपोर्ट करता हूँ... और लैपटॉप कहता है—"अब नहीं यार!"

इसीलिए बायोइन्फॉर्मेटिक्स में लगता है समय,
ये “बस सीरत चलाओ” या “वोल्कैनो प्लॉट बनाओ” नहीं है।
ये है सिस्टम एडमिन का काम, डेटा की सफ़ाई,
QC, डिबगिंग, और सांइस की सच्ची लड़ाई।

तो कुछ सीखें इस व्यथा से आप भी आज:
24 घंटे पहले चमत्कार मत माँगिए।
अच्छे फ़िगर साफ़ डेटा से बनते हैं।
बायोइन्फॉर्मेटिक्स जादू नहीं, विज्ञान है।
समय से बात कीजिए, प्रक्रिया का सम्मान कीजिए।

और उन सभी बायोइन्फॉर्मेटिशियनों को सलाम,
जो दूसरों की प्रेज़ेंटेशन के लिए रातों में जागते हैं—
तुम हो फ़िगर्स के भूत लेखक,
तुम हो बिना नाम के सह-लेखक।
तुम पहले लेखक बनने के हक़दार हो—
और एक लंबी नींद के भी।

Note: Written with the help of AI/LLM Tools !

Rdatamining.com : R and Data Mining

Poonam Mahapatra — Thu, 15 Aug 2013 18:37:23 -0500

This website presents examples, documents and resources on data mining with R.
Documents on using R for data mining are available to download for non-commercial personal use, including R Reference card for Data Mining, R and Data Mining: Examples and Case Studies and Time Series Analysis and Mining with R.

Address of the bookmark: http://www.rdatamining.com/

Courses to Get You Started with Bioinformatics

LEGE — Tue, 30 Sep 2025 13:07:19 -0500

Bioinformatics is now at the heart of modern biology and medicine. From decoding genomes and predicting antimicrobial resistance, to developing personalized medicine and advancing evolutionary research, computational skills are no longer optional — they are essential.

Yet, for many students, biologists, and even computer scientists, the question is: “Where do I begin?” With so many platforms, books, and tutorials available, it’s easy to feel overwhelmed.

To make it easier, I’ve compiled 10 excellent resources — ranging from beginner-friendly introductions to advanced computational genomics courses. Many of these are freely available, created by pioneers in the field, and widely used in classrooms and research labs worldwide.

Whether you are a complete beginner or looking to strengthen your foundations, these courses will help you build the skills needed to analyze biological data, design workflows, and think computationally about complex biological systems.