BOL: Related items

MetaPred2CS

Manisha Mishra — Fri, 03 Mar 2017 05:15:07 -0600

MetaPred2CS Web server is a meta-predictor based on Support Vector Machine (SVM) that combines 6 individual sequence based protein-protein interaction prediction methods to predict prokaryotic two-component system protein-protein interactions (PPIs). The methods implemented in MetaPred2CS are 2 co-evolutionary methods: in-silico two hybrid (i2h) and mirror tree (MT) methods and 4 genomics context based methods: phylogenetic profiling (PP), gene fusion (GF), gene neighbourhood (GN) and and gene operon methods (GO).

http://metapred2cs.ibers.aber.ac.uk/

Address of the bookmark: https://github.com/martinjvickers/MetaPred2CS

Foldit: Solve Puzzles for Science

Robert M Willioms — Thu, 21 Dec 2017 15:17:47 -0600

Foldit is an online puzzle video game about protein folding. It is part of an experimental research project developed by the University of Washington, Center for Game Science, in collaboration with the UW Department of Biochemistry. The objective of Foldit is to fold the structures of selected proteins as perfectly as possible

https://fold.it/portal/

Address of the bookmark: https://fold.it/

FANTASIA

BioStar — Wed, 20 Aug 2025 02:48:15 -0500

FANTASIA is an advanced pipeline for the automatic functional annotation of protein sequences using state-of-the-art protein language models. It integrates deep learning embeddings and in-memory similarity searches, retrieving reference vectors from a PostgreSQL database with pgvector, to associate Gene Ontology (GO) terms with proteins.

https://www.nature.com/articles/s42003-025-08651-2

Address of the bookmark: https://github.com/CBBIO/FANTASIA

HapSolo: An optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding.

Jit — Mon, 26 Oct 2020 21:23:36 -0500

Despite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent highly heterozygous regions. If primary and secondary contigs are not properly identified, the primary assembly will overrepresent both the size and complexity of the genome, which complicates downstream analysis such as scaffolding.

More at https://github.com/esolares/HapSolo

Address of the bookmark: https://github.com/esolares/HapSolo

Ten recommendations for creating usable bioinformatics command line software

RAJESH DETROJA — Sun, 08 Jun 2014 10:06:26 -0500

Bioinformatics software varies greatly in quality. In terms of usability, the command line interface is the first experience a user will have of a tool. Unfortunately, this is often also the last time a tool will be used. Here I present ten recommendations for command line software author’s tools to follow, which I believe would greatly improve the uptake and usability of their products, waste less user’s time, and improve the quality of scientific analyses.

Address of the bookmark: http://www.gigasciencejournal.com/content/2/1/15?utm_content=buffer25ee0&utm_medium=social&utm_source=twitter.com&utm_campaign=buffer

Google Genomics

Tenzin Paul — Thu, 18 Dec 2014 11:05:42 -0600

Explore genetic variation interactively. Compare entire cohorts in seconds with SQL-like queries. Compute transition/transversion ratios, genome-wide association, allelic frequency and more.
Process big genomic data easily. Run batch analyses like principal component analysis and Hardy-Weinberg equilibrium on as many samples as you like, in minutes or hours, with just a little code.
Use Google's infrastructure and big data expertise. Store one genome or a million using Google Genomics and take advantage of the same infrastructure that powers Search, Maps, YouTube, Gmail and Drive.
Support emerging global standards. Google Genomics is implementing the API defined by the Global Alliance for Genomics and Health for visualization, analysis and more. Compliant software can access Google Genomics, local servers, or any other implementation.

Address of the bookmark: https://cloud.google.com/genomics/

Enrichr: a comprehensive gene set enrichment analysis

Jit — Thu, 27 Apr 2017 05:42:09 -0500

Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gene set libraries available for analysis and download. In total, Enrichr currently contains 180 184 annotated gene sets from 102 gene set libraries. New features have been added to Enrichr including the ability to submit fuzzy sets, upload BED files, improved application programming interface and visualization of the results as clustergrams. Overall, Enrichr is a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries. Enrichr is freely available at: http://amp.pharm.mssm.edu/Enrichr.

https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw377

Address of the bookmark: http://amp.pharm.mssm.edu/Enrichr/

Installing ELGG on Ubuntu !

Jit — Thu, 25 Nov 2021 01:45:59 -0600

Follow this:

Settings file

Error

Your web server does not have permission to create the settings.php file in your installation directory. You have two choices:

1. Change the permissions on the elgg-config directory of your Elgg installation

2. Copy the file elgg-config/settings.example.php to elgg-config/settings.php and follow the instructions in it for setting your database parameters.

To resolve this --

Change the permision

chmod 777 elgg-config

Web server

Warning

Your server does not support automatic testing of the rewrite rules and your browser does not support checking via JavaScript. You can continue the installation, but you may experience problems with your site. You can manually test the rewrite rules by clicking this link: test. You will see the word success if the rules are working.

create a .httaccess

and provide detail in it

Installation of Elgg

(Note: Elgg requires installing an instance of MySQL.)

Steps to make adjustment and disposal of trial installations easier.

MySQL

At this point, we assume you've set up your MySQL database

Start your mysqld server daemon.
(For the sake of this example, we'll assume we're running on port 9999; you shouldn't actually use this port because only one daemon can run on any port number.)
Login to the server as root user, using the mysql client.
Create a database to store Elgg's tables. We'll call the database elggalpha.
mysql> create database elggalpha;

Grant access to a user — for this example we'll call him/her elggalphauser.

mysql> grant all privileges on elggalpha.* to 'elggalphauser'@'moxie'
    -> identified by 'secretpassword';

Elgg

Type umask 022
Change into your public_html directory (aka folder).
cd public_html
make a directory called elgg
mkdir elgg
Change into the elgg subdirectory of public_html.
cd elgg
download elgg into this directory
you'll end up with a file named
/home/your-user-id/public_html/elgg/elgg-X.X.X.X.zip
(It's not literally X.X.X.X, it might be elgg-1.8.0.1.zip, for example.)
unzip elgg
unzip -q elgg-1.8.0.1.zip
you'll end up with a directory (folder) named
/home/your-user-id/public_html/elgg/elgg-X.X.X.X
make a symbolic link (aka shortcut) to this
ln -s elgg-X.X.X.X alpha
(For example, ln -s elgg-1.8.0.1 alpha)
Give user nobody access to this directory
/usr/misc/bin/acl.sh -r -u nobody elgg-1.8.0.1
create a data directory for elgg (get into your home directory first):
```
cd
mkdir -p elgg/alpha/data
chmod -R 755 elgg/alpha/data
```
Change into the elgg/alpha directory.
cd elgg/alpha
Give user nobody access to this subdirectory data
/usr/misc/bin/acl.sh -u nobody data

In your browser, navigate to your elgg installation
http://moxie.cs.oswego.edu/~your-user-id/elgg/alpha/
You'll have a screen which includes this message:

Welcome

Installing Elgg has 6 simple steps and reading this welcome is the first one!

If you haven't already, read through the installation instructions included with Elgg (or click the instructions link at the bottom of the page).

If you are ready to proceed, click the Next button.

Follow configuration process:

The first screen probably will contain a success message in green and a failure message in pink:
```
Requirements check

Your server failed the requirements check. After you have fixed the below issues, refresh this
page. Check the troubleshooting links at the bottom of this page if you need further assistance.
PHP
```
Your server's PHP satisfies all of Elgg's requirements.
```
Web server
```
We think your server is running the Apache web server. The rewrite test failed and the most likely cause is that AllowOverride is not set to All for Elgg's directory. This prevents Apache from processing the .htaccess file which contains the rewrite rules. A less likely cause is Apache is configured with an alias for your Elgg directory and you need to set the RewriteBase in your .htaccess. There are further instructions in the .htaccess file in your Elgg directory.
```
Database
```
The database requirements are checked when Elgg loads its database.
To correct this, replace the .htaccess file that Elgg created with one that you can edit:
```
cp -ip .htaccess temp-htaccess
rm .htaccess
mv temp-htaccess .htaccess
```
Edit the .htaccess file: Go to approximately line 101 (where it says #RewriteBase /) and add the line:
RewriteBase /~your-user-id/elgg/alpha/
Be sure to save the edited file.
Click the Refresh button.
If this hasn't fixed things, seek professional help.
Click the Next button.

Fill in the parameters appropriate to your MySQL installation.

Database installation

If you haven't already created a database for Elgg, do that now. Then fill in the values below to
initialize the Elgg database.

Database Username

elggalphauser

User that has full priviledges to the MySQL database that you created for Elgg

Database Password

secretpassword

Password for the above database user account

Database Name

elggalpha

Name of the Elgg database

Database Host

^‡

moxie:9999

Hostname of the MySQL server (usually localhost)
‡You might need to use 127.0.0.1:9999 for the host
    if you haven't set up MySQL as we've done.



Database Table Prefix

elgg_

The prefix given to all of Elgg's tables (usually elgg_)

Continue filling in forms as requested.

Configure site

Database has been installed.

We need some information about the site as we configure Elgg. If you haven't created a data directory for Elgg, you need to do so now.

Site Name

My Elgg Site version Alpha

The name of your new Elgg site

Site Email Address

your-user-id@oswego.edu

Email address used by Elgg for communication with users

Site URL

http://moxie.cs.oswego.edu/~your-user-id/elgg/alpha/

The address of the site (Elgg usually guesses this correctly)

Elgg Install Directory

/home/your-user-id/public_html/elgg/elgg.1.8.0.1/

The directory where you put the Elgg code (Elgg usually guesses this correctly)

Data Directory

/home/your-user-id/elgg/alpha/data

The directory that you created for Elgg to save files (the permissions on this directory are checked
when you click Next)

Default Site Access

Public

The default access level for new user created content

Create admin account

Site settings have been saved.

It is now time to create an administrator's account.

Display Name

The name that is displayed on the site for this account

Email Address

Username

Account username used for logging in

Password

Account password must be at least 6 characters long

Password Again

Retype password to confirm

Stay Connected and Productive: Unlock the Power of Screen, Tmux, and Mosh for Bioinformatics

BioStar — Wed, 22 Jan 2025 00:29:52 -0600

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:

Start a Session:

screen
Detach from a Session:
Press Ctrl+A, then D.
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:

Start a Session:

tmux
Detach from a Session:
Press Ctrl+B, then D.
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:

Install Mosh:

sudo apt install mosh # For Debian/Ubuntu
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!

Bioinformatics web development course

Jit — Wed, 06 Nov 2019 20:42:48 -0600

This web development course, targeted at Biology and Bioinformatics students, aims at teaching from scratch all the skills needed to setup a fully working Linux web server and to develop and deploy web applications for Bioinformatics.

No previous programming knowledge is assumed. By following this tutorial you will learn the fundamental concepts of programming by using scripting languages: variables, types, arrays, cycles, conditional statements, functions, objects, regular expressions, files reading and manipulation et-cetera.

Address of the bookmark: http://www.cellbiol.com/bioinformatics_web_development/introduction/