<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/14800?offset=680 https://bioinformaticsonline.com/blog/view/44762/stay-connected-and-productive-unlock-the-power-of-screen-tmux-and-mosh-for-bioinformatics Wed, 22 Jan 2025 00:29:52 -0600 https://bioinformaticsonline.com/blog/view/44762/stay-connected-and-productive-unlock-the-power-of-screen-tmux-and-mosh-for-bioinformatics <![CDATA[Stay Connected and Productive: Unlock the Power of Screen, Tmux, and Mosh for Bioinformatics]]> If you are a bioinformatician, chances are you have spent hours running long, complex analyses on remote servers only to lose your session because of an unstable connection. Frustrating, isnt it? Fear not! With tools like screen, tmux, and mosh, you can safeguard your workflow and stay productive, no matter where you are.

Why Remote Session Management is a Must-Have

In bioinformatics, tasks like genome assembly, RNA-seq analyses, and phylogenetic computations often take hours or days. A dropped SSH connection can result in:

  • Lost Progress: Restarting a job from scratch wastes valuable time.
  • Workflow Interruptions: Disruptions can derail your focus and productivity.
  • Corrupted Data: Interrupted processes may lead to incomplete or corrupted outputs.

By integrating screen, tmux, or mosh into your workflow, you can avoid these setbacks and ensure a seamless experience.

Screen: The Classic Workhorse

Screen is a terminal multiplexer that comes pre-installed on most Linux systems. It allows you to manage multiple terminal sessions and reconnect to them even after being disconnected.

Getting Started with Screen:

  1. Start a Session:
    screen
  2. Detach from a Session:
    Press Ctrl+A, then D.
  3. Reattach to a Session:
    screen -r

Pro Tip: Enhance your screen experience with a customized .screenrc configuration file. Download one here: Get .screenrc.

Tmux: A Modern Alternative

Tmux takes everything great about screen and adds modern features, including better key bindings and intuitive session management. It\u2019s perfect for bioinformaticians who want more control over their workflow.

Getting Started with Tmux:

  1. Start a Session:
    tmux
  2. Detach from a Session:
    Press Ctrl+B, then D.
  3. Reattach to a Session:
    tmux attach

Customize Your Tmux Experience:
Use a .tmux.conf file to personalize your setup. Grab one here: Download .tmux.conf.

Mosh: The Mobile Shell for Unreliable Connections

SSH works well for stable networks, but it struggles in areas with spotty connectivity. Enter Mosh, the Mobile Shell. Designed for intermittent networks, Mosh keeps your session alive even when the connection drops temporarily.

Why Mosh is a Game-Changer:

  • No lag over high-latency networks.
  • Automatically reconnects when the network is restored.
  • Ideal for working on the go, from cafes to trains.

Getting Started with Mosh:

  1. Install Mosh:
    sudo apt install mosh # For Debian/Ubuntu
  2. Connect to a Server:
    mosh username@server

Learn more at mosh.org.

Why This Matters for Bioinformatics

Every bioinformatician knows the value of time and data integrity. Tools like screen, tmux, and mosh provide a lifeline when running long analyses, enabling you to:

  • Safeguard your work against disconnections.
  • Easily manage multiple workflows in parallel.
  • Stay productive, even in challenging environments.

Quickstart Cheat Sheet

  • Screen:

    screen # Start a session Ctrl+A, D # Detach screen -r # Reattach

  • Tmux:

    tmux # Start a session Ctrl+B, D # Detach tmux attach # Reattach

  • Mosh:

    mosh username@server

Final Thoughts

As a bioinformatician, your time is too valuable to spend restarting analyses due to technical hiccups. With screen, tmux, and mosh in your toolkit, you can work smarter, protect your progress, and stay productive no matter where you are. Start using these tools today and transform the way you work with remote systems.

Let me know how these tools work for you, and don\u2019t forget to follow for more bioinformatics tips!

]]> BioStar https://bioinformaticsonline.com/blog/view/44908/top-journals-in-bioinformatics-how-to-choose-where-to-publish-why-it-matters Fri, 26 Sep 2025 06:49:02 -0500 https://bioinformaticsonline.com/blog/view/44908/top-journals-in-bioinformatics-how-to-choose-where-to-publish-why-it-matters <![CDATA[Top Journals in Bioinformatics: How to Choose Where to Publish & Why It Matters]]>

Bioinformatics is a rapidly growing field at the intersection of biology, computer science, mathematics, and statistics. As data volumes increase, as well as the diversity of data types (genomics, proteomics, metabolomics, imaging, single‑cell data, etc.), the need for robust computational methods, rigorous models, and reproducible tools has never been greater.


A key decision for researchers is: Where should I publish my work? The choice of journal impacts visibility, peer recognition, and long‑term influence of your research. Below I provide a guide to leading journals in bioinformatics, criteria for selecting the journal that best fits your work, and why these considerations matter.

Leading Journals in Bioinformatics

Journal

What it’s Known For / Strengths

Best Fit for What Kind of Work

Bioinformatics (Oxford Journals)

Strong for methods, computational biology, database papers, algorithm development.

New computational methods; tools with broad applicability; databases; methodological advances.

Briefings in Bioinformatics

High impact reviews, overviews, and synthesis articles.

Review‑style articles; comparative studies; widely used tools.

PLOS Computational Biology

Emphasis on method development plus biological insight; open access.

Interdisciplinary work; computational method with biological applications.

BMC Bioinformatics

Broad scope; good for software, pipelines, resources; open access.

Software development; pipelines; data resources; benchmarking.

IEEE Transactions on Computational Biology and Bioinformatics (TCBB)

Rigor in computation, algorithms, performance.

Algorithmic innovations; statistical/computational method work.

BioData Mining

Focused on data mining / ML in biology.

Machine learning / AI applied to biological datasets; predictive models.

Criteria to Use When Choosing a Journal

  • Scope & Audience
  • Impact & Visibility
  • Review Time & Speed
  • Open Access
  • Cost / APCs
  • Reputation vs Practical Fit
  • Reproducibility, Data & Code Sharing Policies
  • Indexing & Reach
  • Quality of the field
  • Accelerating discovery
  • Fair access
  • Credibility & trust
  • Read recent papers in the journal
  • Tailor the manuscript
  • Check the author guidelines
  • Have backup journals ready
  • More emphasis on machine learning / AI
  • Single‑cell, spatial omics, multimodal data
  • Cloud workflows, reproducible pipelines
  • Preprints / open peer review
  • Alternative metrics (software use, downloads, community adoption)

Selecting where to publish in bioinformatics isn’t just about prestige; it’s about reaching the right audience, ensuring your work is usable, and contributing to the field responsibly.

]]> LEGE https://bioinformaticsonline.com/opportunity/view/45115/postdoctoral-fellow-in-genomics-and-comparative-genomics Thu, 09 Apr 2026 02:12:32 -0500 <![CDATA[Postdoctoral Fellow in Genomics and Comparative Genomics]]> Environnement de travail (Work environment):
The successful candidate will join a dynamic research group working
on the ecology and evolution of host'parasite'environment
interactions in non-model organisms, particularly snail vectors and
its trematode parasites. She/He will conduct genomic analyses aimed at
understanding host'parasite coevolution and the genetic architecture
of resistance in the invasive snail Pseudosuccinea columella to the
zoonotic parasite Fasciola hepatica. This thematic line is embedded
within the regional scientific project InvaSnail financed by the
ExposUM initiative from the Montpellier. The position is based in
Montpellier, a vibrant scientific hub in Southern France internationally
recognized for excellence in ecology and evolutionary biology. The IHPE
laboratory provides a collaborative research environment with access
to high-performance computing facilities, sequencing platforms, and
strong interdisciplinary interactions across research institutions in
the Montpellier area. University

Main mission:

Develop and implement strategies for whole-genome sequencing of non-model
species
Generate high-quality de novo genome assemblies using short- and long-read
sequencing technologies
Perform genome annotation and structural/functional characterization
Conduct comparative genomic analyses across related species or populations
Design and implement genome-wide association studies (GWAS) to identify
loci associated with phenotypic or adaptive traits
Integrate genomic, phenotypic, and environmental datasets
Contribute to the development of reproducible bioinformatics pipelines

Activités (Activities):

Lead the genomic component of the research project
High-molecular-weight DNA extraction optimization
Long-read genome assembly (PacBio HiFi / ONT)
Genome polishing and quality assessment (BUSCO, QUAST)
Structural and functional annotation
Variant discovery (SNPs, indels, SVs)
Population genomic analyses (FST, demographic inference)
Mixed-model GWAS accounting for structure
Workflow development (Snakemake/Nextflow)
HPC-based pipeline implementation
Publish results in peer-reviewed journals
Present findings at international conferences
Collaborate with experimental and computational team members
Contribute to project development
Mentor graduate students when appropriate

More at https://evol.mcmaster.ca/brian/evoldir/PostDocs//MontpellierU.ComparativeGenomics

]]> https://bioinformaticsonline.com/fun/view/4196/chemical-elements-of-bioinformatics Tue, 03 Sep 2013 16:35:39 -0500 https://bioinformaticsonline.com/fun/view/4196/chemical-elements-of-bioinformatics <![CDATA[Chemical Elements of Bioinformatics]]> You must be familiar with periodic table and colour pattern, but this time you are going to amaze by new elements table by Eagle genomics. Just check it out and have fun :)

http://elements.eaglegenomics.com/

]]> Rahul Agarwal https://bioinformaticsonline.com/pages/view/3889/bioinformatics-and-sequencing-courses-and-workshops Sat, 24 Aug 2013 16:41:26 -0500 https://bioinformaticsonline.com/pages/view/3889/bioinformatics-and-sequencing-courses-and-workshops <![CDATA[Bioinformatics and Sequencing Courses and Workshops]]> Swiss Institute of Bioinformatics (SIB) organises lots of bioinformatics courses covering wide range of topics:

http://www.isb-sib.ch/education/training-courses.html

Canadian bioinformatics also organises various bioinformatics and sequencing courses:

http://bioinformatics.ca/workshops

In addition to above two, EMBI Europe, EMBO Europe, Cold Spring Harbour USA, Wellcome Trust UK and NOVA Europe also organise bioinformatics and sequencing courses annually:

http://www.embl.de/training/events/index.php?p_outstation=ALL

http://www.embo.org/funding-awards/courses-workshops

http://meetings.cshl.edu/courses.html

http://www.wellcome.ac.uk/Education-resources/Courses-and-conferences/Advanced-Courses-and-Scientific-Conferences/Advanced-Courses/index.htm

http://www.nova-university.org/pagetop.cfm?MenySidorTop_id=2&open=7

]]> Rahul Agarwal https://bioinformaticsonline.com/researchlabs/view/5401/the-minerva-research-group-for-bioinformatics-janet-kelso Wed, 09 Oct 2013 12:57:45 -0500 <![CDATA[The Minerva Research Group for Bioinformatics (Janet Kelso)]]> The focus of this group is to use computational approaches to gain an insight into genome evolution in primates.

PNAS papers:
http://www.pnas.org/search?author1=Janet+Kelso&sortspec=date&submit=Submit

Jobs:
http://www.eva.mpg.de/genetics/bioinformatics/jobs.html

Contact:
Kelso Group
Department of Evolutionary Genetics
Max Planck Institute for Evolutionary Anthropology
Deutscher Platz 6
04103 Leipzig
Germany
Email: kelso@eva.mpg.de

]]> https://bioinformaticsonline.com/bookmarks/view/7216/free-math-books Thu, 12 Dec 2013 19:38:34 -0600 https://bioinformaticsonline.com/bookmarks/view/7216/free-math-books <![CDATA[Free math books]]> Bioinformatics require some match skills, therefore I decided to provide this wonderful math eBooks links to the BOL community.

Please add ur links/bookmarks in comment section.

Address of the bookmark: http://physicsdatabase.com/free-math-books/

]]> Manisha Mishra https://bioinformaticsonline.com/bookmarks/view/7387/bioinformatics-software-for-biologists-in-the-genomics-era Sun, 22 Dec 2013 17:31:05 -0600 https://bioinformaticsonline.com/bookmarks/view/7387/bioinformatics-software-for-biologists-in-the-genomics-era <![CDATA[Bioinformatics software for biologists in the genomics era]]> The genome sequencing revolution is approaching a landmark figure of 1000 completely sequenced genomes. Coupled with fast-declining, per-base sequencing costs, this influx of DNA sequence data has encouraged laboratory scientists to engage large datasets in comparative sequence analyses for making evolutionary, functional and translational inferences. However, the majority of the scientists at the forefront of experimental research are not bioinformaticians, so a gap exists between the user-friendly software needed and the scripting/programming infrastructure often employed for the analysis of large numbers of genes, long genomic segments and groups of sequences. We see an urgent need for the expansion of the fundamental paradigms under which biologist-friendly software tools are designed and developed to fulfill the needs of biologists to analyze large datasets by using sophisticated computational methods. We argue that the design principles need to be sensitive to the reality that comparatively small teams of biologists have historically developed some of the most popular biological software packages in molecular evolutionary analysis. Furthermore, biological intuitiveness and investigator empowerment need to take precedence over the current supposition that biologists should re-tool and become programmers when analyzing genome scale datasets.

Address of the bookmark: http://bioinformatics.oxfordjournals.org/content/23/14/1713.full

]]> Poonam Mahapatra https://bioinformaticsonline.com/opportunity/view/20508/15-highly-motivated-early-stage-researchers-esrsphd-positions Sun, 25 Jan 2015 05:23:53 -0600 <![CDATA[15 highly motivated Early Stage Researchers (ESRs)/PhD positions]]> The MiND programme looking for 15 highly motivated Early Stage Researchers (ESRs), researchers with a BSc or MSc degree within the first four years (full-time equivalent) of their research career

All applications sent before 2nd of February 2015.

http://www.mind-project.eu/career

]]> https://bioinformaticsonline.com/opportunity/view/22891/17-marie-curie-phd-position-available-immediately Tue, 23 Jun 2015 06:52:06 -0500 <![CDATA[17 Marie Curie PhD position available immediately]]> Kindly look into following webpage:
http://medhealth.leeds.ac.uk/info/1450/scholarships/1795/marie_curie_phd_training_network

The closing date for application will be 26 June 2015.

]]>