BOL: Related items

Bpipe - a tool for running and managing bioinformatics pipelines

Radha Agarkar — Sat, 21 May 2016 22:42:16 -0500

Bpipe provides a platform for running big bioinformatics jobs that consist of a series of processing stages - known as 'pipelines'.

January 20th, 2016 - New! Bpipe 0.9.9 released!
Download latest, all
Documentation
Mailing List (Google Group)

Bpipe has been published in Bioinformatics! If you use Bpipe, please cite:

Sadedin S, Pope B & Oshlack A, Bpipe: A Tool for Running and Managing Bioinformatics Pipelines, Bioinformatics

Address of the bookmark: http://docs.bpipe.org/

Bioinformatics Head (Bioinformatics Manager III), Cancer Genomics Research Laboratory at Frederick National Laboratory

Wed, 18 Aug 2021 00:19:48 -0500

Frederick National Laboratory seeking an enthusiastic, creative, and seasoned bioinformatics professional to join our leadership team and direct the exceptional Bioinformatics Group at the Cancer Genomics Research Laboratory (CGR). CGR has a diverse team of bioinformatics and computational scientists that support all areas of bioinformatics and data analysis (infrastructure, data QC, pipeline development and maintenance, data curation and sharing, methodology development, statistical analyses, machine learning approaches, and scientific interpretation).

More at https://leidosbiomed.csod.com/ats/careersite/jobdetails.aspx?site=4&c=leidosbiomed&id=2040

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 !

Bioinformatics Scientist, Production Bioinformatics @ South San Francisco, CA

Thu, 19 Aug 2021 08:45:24 -0500

wist is looking for a Bioinformatics Scientist to join our Production Bioinformatics Team. You will work alongside research scientists, software engineers and data scientists to further deliver on our mission to expand access to best-in-class synthetic biology and next-generation sequencing applications. You will be developing and engineering tools to better evaluate and build hardened, production quality pipelines, optimize data quality, and automate lab and bioinformatics processes. Our ideal candidate is an organized problem solver with a background in developing and building novel production-quality bioinformatics tools and packages. Equally excellent communication skills and a proven ability to work independently are required.

More at https://boards.greenhouse.io/twistbioscience/jobs/3135495?gh_src=9ecc0b941us

Amity University Bioinformatics Summer Program - Kolkata

eliabrodsky — Tue, 11 Jun 2019 21:27:10 -0500

Registrations are now open for the 2019 Summer Bioinformatics Training program at Amity University, Kolkata. The program will focus on introductory topics for life science students. We will review important history, topics and challenges bioinformatics can help address in the context of basic research, discovery and industry.

Read more: https://edu.t-bio.info/amity-university-summer-bioinformatics-program-registrations-are-open/

Research Associate Bioinformatics in IISc Recruitment 2020

Tue, 23 Jun 2020 21:53:34 -0500

Research Associate Bioinformatics in IISc Recruitment 2020

Essential Qualifications: Ph.D. (Bioinformatics/ Biophysics/ Biotechnology or any other stream of biological/ physical sciences) with a minimum of two publications in reputed peer reviewed journals in the area of structural bioinformatics or biophysics or biomolecular modeling/ simulation.

Job description: Development of bioinformatics tools and algorithms/software for structure based analysis of biomolecular systems. Programmatic access to major biomolecular databases using APIs Knowledge based prediction and analysis of biomolecular structure, function and interactions. Docking/simulations for inhibitor design.

Desirable Qualifications (Research Associate/s): i) Strong computer programming skills (in Python/PERL/PHP or C++ or object oriented database management systems like MySQL etc or scripting languages under LINUX/UNIX environment).

ii) Extensive experience in computational analysis of biomolecular structure/interactions and usage of advanced biomolecular simulation softwares. iii) Adequate knowledge of major databases, webservers and softwares in the area of biomolecular structure/function and drug design. iv) Familiarity with Parallel Programming environments and experience in usage of high-end HPC clusters.

The candidates must highlight their experience in above mentioned fields/topics in their CV. Initial appointment will be for a period of 1 year, subject to extension after review of performance.

Emoluments: As per DST, GOI norms and commensurate with experience.

More at https://www.iisc.ac.in/positions-open/

BioGPS

Anjana — Mon, 23 May 2016 03:15:46 -0500

A free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function.

http://biogps.org/#goto=welcome

Address of the bookmark: http://biogps.org/#goto=welcome

ClueGO

Jit — Thu, 02 Jun 2016 09:51:44 -0500

ClueGO is a Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network and it can be used in combination with GOlorize.

Address of the bookmark: http://www.ici.upmc.fr/cluego/

methylKit

Jit — Fri, 03 Jun 2016 10:09:29 -0500

methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods such as Agilent SureSelect methyl-seq. In addition, methylKit can deal with base-pair resolution data for 5hmC obtained from Tab-seq or oxBS-seq. It can also handle whole-genome bisulfite sequencing data if proper input format is provided.

Address of the bookmark: https://github.com/al2na/methylKit

4DGenome

Jitendra Narayan — Mon, 04 Jul 2016 00:44:55 -0500

Records in 4DGenome are compiled through comprehensive literature curation of experimentally-derived and computationally-predicted interactions. The current release contains 4,433,071 experimentally-derived and 3,605,176 computationally-predicted interactions in 5 organisms. Experimental data cover both high throughput datasets and individiual focused studies.

All interaction data are freely available in a standardized file format. Records can be queried by genomic regions, gene names, organism, and detection technology.

Address of the bookmark: http://4dgenome.research.chop.edu/