BOL: Related items

Innovative blog and portfolio website!

Surabhi Chaudhary — Tue, 22 Jun 2021 08:30:37 -0500

Do you ever feel overwhelmed or frightened by browsing through someone else's beautiful, responsive portfolio website links and wishing you could create one for yourself?

So there you have it!
Read all the way to the end for a step-by-step guide on creating your own designer portfolio website in under an hour!

Here is the list of useful pages to mativate you

https://brittanychiang.com/

https://ashutosh1919.github.io/#/

https://dalinhuang99.github.io/

http://www.rleonardi.com/interactive-resume/

https://ecoevogeno.org/

https://colauttilab.github.io/

https://github.com/ashutosh1919/masterPortfolio

Free templates at https://html5up.net/

Check Linux server configuration !!

Rahul Nayak — Tue, 06 May 2014 01:10:57 -0500

Bioinformatician uses servers for computational analysis. Sometime we need to check the server details before running our programs or tools. Here I am showing some basic commands using them you can gather the system/server information.

To check what version of Operating System is installed on the server you can use the following commands:-
=================================================================
1.cat /etc/issue
[root@localhost ~]# cat /etc/issue
Red Hat Enterprise Linux Server release 5.5 (Tikanga)
Kernel \r on an \m

2.cat /etc/redhat-release
[root@localhost ~]# cat /etc/redhat-release
Red Hat Enterprise Linux Server release 5.5 (Tikanga)

3.lsb_release -a
[root@localhost ~]# lsb_release -a
LSB Version:    :core-3.1-ia32:core-3.1-noarch:graphics-3.1-ia32:graphics-3.1-noarch
Distributor ID: RedHatEnterpriseServer
Description:    Red Hat Enterprise Linux Server release 5.5 (Tikanga)
Release:        5.5
Codename:       Tikanga

To check whether the operating system is 32 or 64bit:-
================================
# uname -i
[root@localhost ~]# uname -i
i386
(i386 represents that server is having 32bit operating system)

[root@localhost ~]# uname -i
x86_64
(x86_64 represents that server is having 64bit operating system)

To see the processor/CPU information:-
=============================
# cat /proc/cpuinfo
[root@localhost ~] cat /proc/cpuinfo
processor       : 0
vendor_id       : GenuineIntel
cpu family      : 6
model           : 15
model name      : Intel(R) Xeon(R) CPU            5130 @ 2.00GHz
stepping        : 6
cpu MHz         : 1995.087
cache size      : 4096 KB
physical id     : 0
siblings        : 2
core id         : 0
cpu cores       : 2
apicid          : 0
fdiv_bug        : no
hlt_bug         : no
f00f_bug        : no
coma_bug        : no
fpu             : yes
fpu_exception   : yes
cpuid level     : 10
wp              : yes
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe nx lm constant_tsc pni monitor ds_cpl vmx tm2 ssse3 cx16 xtpr lahf_lm
bogomips        : 3990.17
(Here processor number 0 indicates that the system is having one process(processor number starts with zero))

To check memory information:-
===========================
# free -m
[root@localhost ~]# free -m
             total       used       free     shared    buffers     cached
Mem:          5066       3513       1552          0        612       2319
-/+ buffers/cache:        582       4484
Swap:         1983          0       1983

# cat /proc/meminfo
[root@localhost ~]# cat /proc/meminfo
MemTotal:      5187752 kB
MemFree:       1639300 kB
Buffers:        627024 kB
Cached:        2374944 kB
SwapCached:          0 kB
Active:        2458788 kB
Inactive:       920964 kB
HighTotal:     4325164 kB
HighFree:      1561936 kB
LowTotal:       862588 kB
LowFree:         77364 kB
SwapTotal:     2031608 kB
SwapFree:      2031608 kB
Dirty:             704 kB
Writeback:           0 kB
AnonPages:      377892 kB
Mapped:          35328 kB
Slab:           153036 kB
PageTables:       6316 kB
NFS_Unstable:        0 kB
Bounce:              0 kB
CommitLimit:   4625484 kB
Committed_AS:   977132 kB
VmallocTotal:   116728 kB
VmallocUsed:      4492 kB
VmallocChunk:   112124 kB
HugePages_Total:     0
HugePages_Free:      0
HugePages_Rsvd:      0
Hugepagesize:     2048 kB

To check the model and serial name of the server:-
=======================================
[root@localhost ~]# dmidecode | egrep -i "product name|Serial number"
Product Name: PowerEdge R710
Serial Number: AB8CDE1


To check the host name:-
=====================
[root@localhost ~]# uname -n
localhost

[root@localhost ~]# hostname
localhost

To check the kernel version:-
========================
[root@localhost ~]# uname -r
2.6.18-238.9.1.el5PAE

Bioinformatician's summer vacation !!!

Jit — Wed, 03 Sep 2014 13:11:50 -0500

Yes, the bioinformatician do spend their summer vacation like this. They spend more time on cheking the JOBS running on various servers.

SLURM

Jit — Wed, 04 May 2016 05:13:21 -0500

SLURM workload manager software, a free open-source workload manager designed specifically to satisfy the demanding needs of high performance computing.

This page is a HOWTO guide for setting up a SLURM installation, currently focused on a CentOS 7 Linux OS. Please send feedback to Ole.H.Nielsen /at/ fysik.dtu.dk.

See the SLURM homepage (also https://computing.llnl.gov/linux/slurm/).

Address of the bookmark: https://wiki.fysik.dtu.dk/niflheim/SLURM

Binding Site Prediction in Protein !

Poonam Mahapatra — Wed, 25 Apr 2018 04:35:57 -0500

The interaction between proteins and other molecules is fundamental to all biological functions. In this section we include tools that can assist in prediction of interaction sites on protein surface and tools for predicting the structure of the intermolecular complex formed between two or more molecules (docking).

Pockets Identification

CASTp

Automatic Identification of pockets and cavities in proteins structure, and quantitation of their volumes using Delaunay triangulation. Available also as PyMOL plugin

Pocket-Finder

Automatic identification of pockets and cavities in proteins structure, and quantitation of their volumes.

PocketPicker

Grid-based technique for the analysis of protein pockets. PocketPicker available as a plugin for PyMOL

Binding Site Prediction

ConSurf

Identification of functional regions in proteins by surface-mapping of phylogenetic information

CRESCENDO

Identification protein interaction sites. It uses sequence conservation patterns in homologous proteins to distinguish between residues that are conserved due to structural restraints from those due to functional restraints.

Ligand Binding Sites

3DLigandSite

The server utilizes protein-structure prediction to provide structural models of the binding site. Ligands bound to structures are superimposed onto the model and use to predict the binding site.

FINDSITE

A threading-based method for ligand-binding site prediction and functional annotation based on binding-site similarity across superimposed groups of threading templates.

LIGSITE^csc

Prediction of binding site by pocket identification using the Connolly surface and degree of conservation

metaPocketA meta server for ligand-binding site prediction. metaPocket use LIGSITE^csc, PASS, Q-SiteFinder and SURFNET

Heatmap Draw !

BioStar — Mon, 06 Mar 2023 04:24:57 -0600

Server for heatmap generation !

https://software.broadinstitute.org/morpheus/

Address of the bookmark: https://software.broadinstitute.org/morpheus/

FRODOCK 2.0: fast protein–protein docking server

Neel — Wed, 17 Oct 2018 04:31:30 -0500

frodock: a user-friendly protein–protein docking server based on an improved version of FRODOCK that includes a complementary knowledge-based potential. The web interface provides a very effective tool to explore and select protein–protein models and interactively screen them against experimental distance constraints. The competitive success rates and efficiency achieved allow the retrieval of reliable potential protein–protein binding conformations that can be further refined with more computationally demanding strategies.

Address of the bookmark: http://frodock.chaconlab.org/

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/

CSAR-web: a web server of contig scaffolding using algebraic rearrangements

BioStar — Fri, 10 Apr 2020 04:39:36 -0500

CSAR-web is a web-based tool that allows the users to efficiently and accurately scaffold (i.e. order and orient) the contigs of a target draft genome based on a complete or incomplete reference genome from a related organism.

CSAR-web can serve as a convenient and useful scaffolding tool allowing the users to efficiently and accurately scaffold their draft genomes according to a complete or incomplete reference genome.

Address of the bookmark: http://genome.cs.nthu.edu.tw/CSAR-web

htop explained

Jit — Wed, 06 Jul 2022 01:28:09 -0500

For the longest time I did not know what everything meant in htop.

I thought that load average 1.0 on my two core machine means that the CPU usage is at 50%. That's not quite right. And also, why does it say 1.0?

I decided to look everything up and document it here.

Address of the bookmark: https://peteris.rocks/blog/htop/