User:Jarle Pahr/Software

Notes on software of interest:

Software development

https://www.docker.io/

http://hpcugent.github.io/easybuild/

http://dirkgorissen.com/2012/09/13/the-research-software-engineer/

http://nvie.com/posts/a-successful-git-branching-model/

http://www.amazon.com/Introduction-Development-Assurance-Management-ebook/dp/B00D0ASZ9K/ref=sr_1_19?ie=UTF8&qid=1376608892&sr=8-19&keywords=software+development

http://www.amazon.com/Code-Complete-Practical-Handbook-Construction/dp/0735619670/ref=sr_1_5?ie=UTF8&qid=1376608312&sr=8-5&keywords=software+development

http://pragprog.com/book/ltp2/learn-to-program

http://pragprog.com/book/tpp/the-pragmatic-programmer

http://www.basilv.com/psd/blog/2007/top-five-essential-practices-for-developing-software

http://codebalance.blogspot.no/2011/02/20-software-developing-best-practices.html

Prlić A, Procter JB (2012) Ten Simple Rules for the Open Development of Scientific Software. PLoS Comput Biol 8(12): e1002802.

http://ivory.idyll.org/blog/blog-review-criteria-for-bioinfo.html

http://ivory.idyll.org/blog/top-ten-things-i-hate-about-bioinfo-software.html

Maintenance & Availability

Obituaries for bioinformatics tools. http://blog.openhelix.eu/?p=12206

http://www.biostars.org/p/44043/

Schultheiss, Sebastian J., et al. "Persistence and availability of web services in computational biology." PLoS one 6.9 (2011): e24914.

http://sciencecodemanifesto.org/

Molecular modelling

http://www.quantum-espresso.org/download/

Open Source resources

http://www.ohloh.net/

iGEM related

http://igem.synbioreview.com/

Web hosting/Servers/Wiki

http://lifehacker.com/126052/geek-to-live--how-to-host-a-personal-wiki-on-your-home-computer

Misc

GeneDesign: http://54.235.254.95/gd/index.html

Genomespace: http://www.genomespace.org/what-is-genomespace

4peaks: http://nucleobytes.com/index.php/4peaks/

https://evernote.com/

Search engine: http://www.vadlo.com/

SAGE notebook: http://nb.sagemath.org/

Software lists:

http://en.bio-soft.net/dna.html

CLC Free workbench: http://www.selectscience.net/products/clc-free-workbench-software/?prodID=20301&u=C1DCA37C-1E5D-4BBF-9283-CAB91EF71E0B&techBID=112&utm_source=social&utm_medium=researchgate&utm_campaign=product

Galaxy: https://main.g2.bx.psu.edu/

Productivity tools & Project management

http://sourceforge.net/projects/openworkbench/

Chromatogram viewers

Seqtrace: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413935/

4peaks

FinchTV

CodonCode aligner

Molecular cloning

Plasmidomics: http://www.ira.cinvestav.mx/Investigaci%C3%B3n/Biotecnolog%C3%ADayBioqu%C3%ADmica/ProfesoresInvestigadores/DrRobertWinkler/Software/PlasmidDrawingProgramPlasmidomics02/tabid/778/language/en-US/Default.aspx

Genestudio: http://sourceforge.net/projects/genestudio/?source=directory

A plasmid Editor: http://openwetware.org/wiki/ApE_-_A_Plasmid_Editor_%28software_review%29

http://biologylabs.utah.edu/jorgensen/wayned/ape/

Oligator: http://gcat.davidson.edu/igem10/

http://research.med.helsinki.fi/plasmadna/

GENTLE: http://ec2-23-20-169-157.compute-1.amazonaws.com/test/

http://gentle.synbiota.ca/

Plasmid IO: https://plasmid.io/?referral_code=e1772689a533f3f19ea235854cd5689d

CloneManager:

What it does well:

• Plan/perform in silico cloning by restriction digestions and ligations.

What's annoying:

• Plasmid map easily gets cluttered.
• When performing a sequence search, hits are marked, but not selected.
• Not possible to select sequence in multiple alignment result view.
• Annotated view only possible in combination with single-stranded view.
• No option for batch processing (perform the same cloning strategy several times, with different molecules) (?)

How to perform multiple alignment in Clone Manager:

Serial Cloner:

http://serialbasics.free.fr/Serial_Cloner.html

Sequencing/genome assembly

SeqAnswers - Software packages for next gen sequence analysis: http://seqanswers.com/forums/showthread.php?t=43

SAM Tools:

http://samtools.sourceforge.net/

http://samtools.sourceforge.net/samtools.shtml

Bowtie:

http://seqanswers.com/forums/showthread.php?t=706

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome: http://genomebiology.com/2009/10/3/R25

http://bowtie-bio.sourceforge.net/index.shtml

Bowtie vs. BWA: http://seqanswers.com/forums/showthread.php?t=15200

Short Oligonucleotide Alignment Package (SOAP):

http://soap.genomics.org.cn/

Description from SeqAnswers: "A program for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. The updated version uses a BWT. Can call SNPs and INDELs. Author is Ruiqiang Li at the Beijing Genomics Institute."

The initial version, SOAP v1, is a program for gapped and ungapped alignment of short reads to a reference sequence. SOAP has been expanded to a package with several new programs, including:

• SOAPdenovo, "a short read de novo assembly tool, is a package for assembling short oligonucleotide into contigs and scaffolds."
• SOAPaligner/soap2
• SOAPsnp
• SOAPindel

Burrows-Wheeler Aligner (BWA):

" a software package for mapping low-divergent sequences against a large reference genome"/ http://bio-bwa.sourceforge.net/)

Three algorithms:

• BWA-backtrack (Reads up to 100 nt)
• BWA-SW (For longer reads: 70 nt - 1Mb)
• BWA-MEM (For longer reads: 70 nt - 1 Mb. Faster and more accurate than BWA-SW)

BWA is an aligner only, and does not call SNPs or other variations.

Article: Fast and accurate short read alignment with Burrows-Wheeler transform: http://www.ncbi.nlm.nih.gov/pubmed/19451168

Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM: http://arxiv.org/abs/1303.3997

Assembly By Short Sequences (ABySS):

http://www.bcgsc.ca/platform/bioinfo/software/abyss

"A de novo, parallel, paired-end sequence assembler."

Euler-SR:

https://ngslib.genome.tugraz.at/node/64

Genome/sequence data analysis

Sequence Assembly Manager (SAM): http://www.bcgsc.ca/platform/bioinfo/software/sam

http://g6g-softwaredirectory.com/

Description: "SAM is a Whole Genome Assembly (WGA) Management and Visualization Tool. It provides a generic platform for manipulating, analyzing and viewing WGA data, regardless of input type."

Integrative Genomics Viwer: http://www.broadinstitute.org/software/igv/home

Open Genomics Engine: http://www.opengenomicsengine.org/learn/

DNAsp: http://bioinformatics.oxfordjournals.org/content/25/11/1451

http://www.jalview.org/

Rapid Identification of Non-human Sequences (RINS): http://khavarilab.stanford.edu/resources.html

Management and planning

http://sourceforge.net/projects/mindraider/?source=directory

Misc

DAMBE5: A Comprehensive Software Package for Data Analysis in Molecular Biology and Evolution: http://mbe.oxfordjournals.org/content/30/7/1720.full

http://www.bioconductor.org/

FASTA software package: http://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml

GeneDesign: http://54.235.254.95/gd/

Artemis:

What it does well:

• Hookup to BLAST search.
• Mark ORFs.
• View all reading frames simultaeneously.

What's annoying:

• Somewhat cumbersome interface.
• Confusing file-handling (how to load/save files).

Wishlist: A program able to perform batch in silico cloning. Example scenario:

• Define several sequences. Use the program to define oligomers for SOE PCR construction of these sequences.
• Define restriction site linkers to append to every sequence, and which are automatically appended to the primers.

Systems Biology

Cytoscape

http://cytoscape.org/

Plugins/apps:

From Cytoscape 3.0, plugins are known as apps. 2.x plugins do not work with Cytoscape 3.x The NetworkAnalyzer plugin for CytoScape 2.x is included as part of the Cytoscape 3.x core.

CytoScape App store: http://apps.cytoscape.org/

ContigScape An interactive guidance tool for microbial genome gap closure

Publications

Source Code for Biology and Medicine: http://www.scfbm.org/