BOL: Related items

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 !

PhD at National Institute for Research in Reproductive Health

Fri, 30 Aug 2013 04:50:35 -0500

National Institute for Research in Reproductive Health

(Indian Council of Medical Research )
Jehangir Merwanji Street, Parel, Mumbai 400 012

Advertisement No. 1/NIRRH/Ph.D. 2013
Admission to Ph.D. Programme – 2013

National Institute for Research in Reproductive Health, Mumbai, a premier institute of the Indian Council of Medical Research, conducts basic, clinical and operational research in different areas of reproductive health. The thrust areas of research include: Fertility Regulation, Infertility and Reproductive Disorders, Reproductive Tract Infections, Maternal and Child Health, Osteoporosis, Genetic Disorders, Stem Cell Biology, Structural Biology, Bioinformatics and Reproductive Toxicology. Institute is affiliated to the University of Mumbai for the award of Ph.D. degree in Applied Biology, Biochemistry, Life Sciences and Biotechnology. The institute invites applications from young and bright students for enrollment in Ph.D. programme.

More at http://www.nirrh.res.in/announcements/phd_program_2013.htm

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.

1. HarvardX Data Analysis for Genomics by Rafael Irizarry

From the almighty Rafa, this set of online courses (via edX/HarvardX) is a classic starting point for genomic data science and bioinformatics.

2. Applied Computational Genomics – Aaron Quinlan

Aaron Quinlan (creator of bedtools and many other tools) has made his course materials open. A practical, tool-driven genomics introduction.

3. Bioinformatics Algorithms (Coursera + Companion Book)

Find the highly visual video classes on Coursera, backed by the popular Bioinformatics Algorithms book.

4. The Biostar Handbook

Not a course per se, but a hands-on manual by Istvan (founder of Biostars.org) that’s even used in classes at Penn State.

5. Introduction to Bioinformatics and Computational Biology (by Shirley Liu)

A comprehensive introduction from Shirley Liu’s lab (Harvard DFCI). Covers both theory and computational practice.

6. Data Carpentry: Genomics Workshops

Community-driven training workshops that focus on practical, reproducible research. I was honored to serve as curriculum committee chair here.

7. Computational Genomics: Applied Comparative Genomics

From the Schatz Lab — applied comparative genomics with real-world data.

8. Introduction to Computational Biology (Mike Love, creator of DESeq2)

This course bridges statistics, biology, and computation — a solid primer for anyone entering computational biology.

9. MIT Computational Biology (6.047 / 6.878 / HST.507) by Manolis Kellis

Covers genomes, networks, evolution, and health. A deep-dive from MIT’s OpenCourseWare archive.

10. An Introduction to Applied Bioinformatics

An interactive textbook with Python code, designed for practical applied bioinformatics learning.

Look up a biological numbers

Jitendra Narayan — Fri, 23 Aug 2013 03:27:45 -0500

Did you ever need to look up a number like the volume of a cell or the cellular concentration of ATP, only to find yourself spending much more time than you wanted on the Internet or flipping through textbooks - all without much success?

Well, it didn’t happen only to you. It is often surprising how difficult it can be to find concrete biological numbers, even for properties that have been measured numerous times. To help solve this for one and all, BioNumbers (the database of key numbers in molecular biology) was created. Along with the numbers, you'll find the relevant references to the original literature, useful comments, and related numbers.

To cite BioNumbers please refer to: Milo et al. Nucl. Acids Res. (2010) 38: D750-D753. When using a specific entry from the database it is highly recommended that you also specify the BioNumbers 6 digit ID, e.g. "BNID 100986, Milo et al 2010".

Address of the bookmark: http://bionumbers.hms.harvard.edu/

Great Place to Study Bioinformatics in Europe

Rahul Agarwal — Sun, 18 Aug 2013 18:41:34 -0500

Study bioinformatics is like being jack of all trade so it is important you choose where it will be good backup of computer science, and natural science infrastructure and faculty. Especially having a good teachers in computer science is indispensible.

Few places in Europe where good (and @some places no tution fees) master bioinformatics courses and recommended are:

KU Leuven, Belgium

http://onderwijsaanbod.kuleuven.be/opleidingen/e/CQ_50269018.htm

ETH, Zurich

http://www.cbb.ethz.ch/

University of Copenhagen, Denmark

http://studies.ku.dk/masters/bioinformatics/

University of Helsinki, Finland

http://www.cs.helsinki.fi/en/mbi/

Stockholm University, Sweden

http://www.sbc.su.se/masters/

Universities in Netherlands

http://www.nbic.nl/education/msc-programmes/

TUM , Munich Germany

http://www.mastersportal.eu/studies/865/bioinformatics.html

University of Bergen, Norway

http://www.uib.no/en/studieprogram/MAMN-INF/BI/plan

Goethe-University in Frankfurt am Main

http://www.uni-frankfurt.de/58444439/mabi

Other links:

http://www.masterstudies.com/Masters-Degree/Bioinformatics/Europe/

https://studyinsweden.se/programmes/?query=bioinformatics&period=ht-2016&level=ma&subject=natural-science&university=#search

Ancestor at work !!!

Jit — Sun, 25 Aug 2013 19:45:28 -0500

When they will learn Bioinformatics :)

SocBiN Bioinformatics 2014

Tue, 03 Sep 2013 18:50:20 -0500

14th annual conference in Bioinformatics

Date : June 10-13

Organizers: The Society for Bioinformatics in Northern European countries (SocBiN) and the Norwegian Bioinformatics Platform / ELIXIR.NO

Venue: Department of Informatics, University of Oslo, Norway

Topics:
Tools and technologies for integrative bioinformatics
Metagenomics
Comparative genomics and phylogeny
Post-ENCODE bioinformatics
Gene regulation
Cancer genomes
Marine genomics

Bioinformatics infrastructure speed up Indian agriculture

Rahul Agarwal — Tue, 07 Jan 2014 12:44:44 -0600

"Realizing the paradigm shift it can bring about, the government is focusing on increased bioinformatics intervention in agri-sciences. Currently under process, the national grid on bioinformatics is expected make much better sense out of huge genomic" -

http://www.biospectrumindia.com/biospecindia/features/203849/supercomputing-indian-agriculture-fast-track-mode/page/1

CPCRI Kasaragod Bioinformatics PA

Sat, 07 Sep 2013 14:15:53 -0500

CENTRAL PLANTATION CROPS RESEARCH INSTITUTE
(Indian Council of Agricultural Research)
KASARAGOD -671 124, KERALA

WALK-IN-INTERVIEW

Walk-in-test cum interview for selection to the following temporary assignments sanctioned under the DBT sponsored adhoc time bound research scheme entitled "Establishment of a Sub-DIC" will be held at CPCRl, Kudlu PO, Kasaragod District, Kerala -6711 24 on the date and time indicated against each:

Project Assistant

Qualification: Essential: Masters Degree in Bioinformatics / B.Tech Degree in Bioinformatics

Desirable: 1. Experience in the field of bioinformatics
2. M.Phil / Doctoral degree in the field

Date of interview 24.09.2013 at 10.00 a.m.

Trainee – 2 Posts

Essential: Masters Degree in Bioinformatics or B.Tech Degree in Bioinformatics.

Date of interview 25.09.2013 at 10.00 a.m.

Studentship – 2 Posts

Essential Final Year/Semester students of MSc Bioinformatics or B.Tech Bioinformatics

Date of Interview 25.09.2013 at 10.00 a.m.

The candidates fulfilling the above eligibility criteria for Item No.1 & II shall apply online and walk-in for a written test and interview at CPCRI, Kasaragod on the respective dates at 10.00 a.m. The candidates for Studentship should submit the application through their Head of the Department. They shall also bring with them a set of bio data and original certificates in proof of age, educational qualifications, experience etc. Candidates who fail to produce the original of the Degree/PO certificates OR provisional certificate will not be allowed to attend the test / interview. Those who are qualified in written test will only be permitted to attend the interview.

No TA will be paid for the journey for attending the interview.

Advertisement: http://www.cpcri.gov.in/images/images/opportunity/sep4_opp.pdf