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Wikiomics:Bioinfo tutorial
Wikiomics:Bioinfo tutorial (exercises)
The goal of this document is to provide a set of illustrative cookbook recipes for wet lab biologists. As there is more than one way of performing a given task, it does point to different tools, but it does not even try to become a yet another directory of links.
You are strongly encouraged to post your comments/ideas on the discussion page of this tutorial.
Before you start
- use text files/plain e-mail whenever possible
- give meaningful names to your files (i.e. humP53_XP12345.fas)
- do not use spaces or Unix special characters in file names (!?"'%&^~*$|/\{}[]()<>:)
- create separate folders/directories for each project with meaningful names
- do not waste paper for printing out your blast search results or sequences
- if primary data needs to be archived burn it on CD using (if possible) non vendor-specific data format
Operating systems/General software
For installing standalone bioinformatics programs the order of preference is: Linux/Unix > MacOS > Windows
Once you move from worksation to bioinformatics application server (almost always Linux/Unix) then as long as you have a Xwindows connection (preferably ssh tunneled) operating system of client workstation plays a minor (if any) role.
DNA sequence processing
Sequence formats
There are multiple sequence formats commonly used. These can be divided into text-only and binary formats.
Unaligned sequences
- Raw sequence ( example) The text file contains nothing but sequence. The information that's inside has to be encoded in the name of the file. Some web servers still require it.
- FASTA (description, example) The most commonly used format (by programs/servers). It can contain either single or multiple sequences, each having a name line, also known as the header, starting with ">" in the first column. Keep in mind that various programs/servers introduce extra restrictions how the FastA header should look like. The "safe" standard:
- Alphanumeric characters only [a-z, A-Z, 0-9], avoid spaces!
- Keep the names short [i.e. 30 characters are significant for clustalw, only 8 for older versions of t_coffee]
- In multiple FastA format keep the names unique
Whenever you plan to analyze your sequence using web servers or command line programs, keep it as FASTA. It is easy to cut the raw sequence out of it, and if your file name/sequence names contain accession numbers to find the GenBank entry.
- GenBank format of choice used by GenBank to display extra information about the sequence. It is fairly complex, but easily readable by humans. Keep your sequences as GenBank when you need extra annotations provided by this format.
- GCG GCG package own format. If you need to use GCG, you will have to convert your sequences into it
- XML eXtended Markeup Language. Standard language slowly taking over the Net. XML files are computer-readable (= information is fairly easy to extract from them) and possible to read by humans. Format of choice when complex sequence information need to be described and computer accessible.
- EXP format used by Wikiomics:Staden sequencing package. Contains both sequence and annotations understandable by Wikiomics:gap4.
- GFF format for (mostly) genomic sequence annotations used by Ensembl [1]
Aligned sequences
- MSF Multiple Sequence Format. Used as output for multiple sequence alignments (pileup from GCG) and as input for alignment editors and shadowing programs.
- ALN standard for multiple sequence alignments. Output format of clustalw and t_coffee.
- PHYLIP used as an input in such programs like PHYLIP package, phyml
- NEXUS advanced format allowing more annotation, used by MrBayes
- ABI binary output format of ABI sequencers. Bulky (= unnecessary large), but so far the only one readable on Mac-OS. Can be easily converted into SCF.
- SCF Sequence Common Format. Standard output for ALF sequencers. More compact than ABI, and commonly used in sequencing projects. Readable on PC and Unix, binary format of the Staden package.
- ZTR successor of SCF with internal data compression. Currently the default binary format for Staden.
Sequence conversion tools
OK for simple format, has problems with aligned sequences
A function in Sean Eddy's SQUID package for converting between unaligned and aligned sequence formats.
can be used for sequence conversion, also for many other bioinformatic related functions.
- for convertions between aligned formats (ALN, MSF, NEXUS, PHYLIP) use:
Processing ABI files and sequence assembly
Before you even start sequencing, plan the way the sequences will be processed. The most important is to establish a proper naming scheme compatible with various programs you (or others) may use downstream for sequence processing. The basic rules for file names are:
- use alphanumeric characters [a-z, A-Z, 0-9]
- use underscore "_" instead of spaces
- full stop shall separate information about sequencing template and primer, like:
Even small sized projects become cumbersome if file names are not unique (you can not assembly files having the same name!). Once these requirements are satisfied, file name alone will give you enough information about:
- whose sample is it?
- to which sequencing project does it belong?
- what was the sequencing template?
- which primer was used?
- was this sample sequenced before?
Programs for DNA sequence assembly
Fasta files (no traces)
- phrap
phrap your_multiple_fasta_file.fa
Results in: your_multiple_fasta_file.fa.contigs
Used for i.e assembly of ESTs.
ABI/SCF files (traces)
- Staden package (Unix, Windows, OSX)
see also another Wikiomics page Wikiomics:Staden
- pregap4 (sequence pre-processing)
Takes a directory or a list of files for preprocessing (creating EXP files, clipping bad quality sequence, marking sequencing vector, repeats etc.
Creating sequence out of ABI chromatogram file is done by a basecalling program. One can go along with ABI-provided basecaller or preferably use:
- phred [2] giving more accurate calls for less accurate part of the sequence (like at the end of the run, say 600bp and more) . Phred also gives a probability/quality values for each of the bases allowing more accurate assembly.
pregap4 %
- gap4 (sequence assembly, editing, verification and much more)
gap4 &
or (to open a specific database at startup):
gap4 database.version.aux &
Other packages:
Vector masking
- EMVEC (web and blast2 based) [4]
Good for a single sequence.
- vectorstrip (Emboss)
vectorstrip -sequence my_fasta_file -vectors my_vectors_fasta_file -mismatch 30 -linkera TAGGATACAG -linkerb TTTTTCAGGACAGACA
- linkera
- 5' sequence
- linkerb
- 3' sequence
- cross_match (from phrap package)
cross_match my_fasta_file my_vectors_fasta_file -minmatch 10 -minscore 20 -screen > screen.out
You will get a file: my_fasta_file.screen --- "devectorised" my_fasta_file
For masking out, let's say, one gene/overlapping clone, etc., type:
cross_match fasta_file_to_be_masked masking_sequence -minmatch 10 -minscore 20 -screen > screen.out
You will get a file: fasta_file_to_be_masked.screen without the sequences matching masking_sequence.
- Figaro
A novel approach for finding putative vector/adapter sequences without knowledge of the vector sequence. "vector sequence is automatically inferred by analyzing the frequency of occurrence of short oligo-nucleotides using Poisson statistics" http://sourceforge.net/apps/mediawiki/amos/index.php?title=Figaro
Masking repetitive sequences using RepeatMasker (WWW/Unix)
- web site: http://www.repeatmasker.org/
- current version (checked on 2010-03.22): 3.2.8
- documentation: http://www.repeatmasker.org/webrepeatmaskerhelp.html
- Online web server [5]
- command line
You have to have a FastA file (it can be multiple FastA). Type:
repmask your_sequence_in_fasta_format
You will get a file: your_sequence_in_fasta_format.masked --- name tells all
species options (choose only one):
-m(us) masks rodent specific and mammalian wide repeats -rod(ent) same as -mus -mam(mal) masks repeats found in non-primate, non-rodent mammals -ar(abidopsis) masks repeats found in Arabidopsis -dr(osophila) masks repeats found in Drosophilas -el(egans) masks repeats found in C. elegans
Primer design
General info about primer design/PCR:
- Primer3plus
- BatchPrimer3 derivative program for designing multiple primers at once
- Pythia new software claiming superiority over primer3
- Oligo (PC & Mac ) $$$, first choice for small projects
- JCVI Primer Designer pipeline primer design for DNA sequencing projects
Also search http://sourceforge.net/ with i.e. "primer pcr" for another, more task specific programs.
- Primer Select from Lasergene (PC & Mac)
DNA -> protein translation
- transeq (Emboss) WWW server
- Protein Translate (ExPasy): WWW server
- ORF Finder WWW server
Cloning in silico
ESTs based
Pre-clustered ESTs:
- STACKdb (limited access, tissue specific splice forms) [6]
- Unigene (no consensus sequence) [7]
- TIGR Gene Indexes
Genome based
- based on homology
- de novo
see also separate page: Wikiomics:Cloning_in_silico
Genome annotation using ESTs assembly
- PASA tool used in many current genome annotation projects
Synthetic genes
Many genes due to an extreme codon bias can not be expressed in model organisms, such as E.coli. To fix this problem one can back-translate protein sequence into nucleotides, using codons preferably used by E.coli. Moreover one can construct sucgh gene from a set of overlapping oligos, introducing restriction sites or other features at will. Programs performing such tasks:
- JCAT http://www.jcat.de/
- GeneDesign
- SGD Syntetic Gene Designer
- Synthetic Gene DataBase [8]
- stand alone program UpGene (SmallTalk) http://www.vectorcore.pitt.edu/upgene/upgene.html
- Codon preference in Pichia pastoris
- Ref
Applied Microbiology and Biotechnology Issue: Volume 67, Number 3 Date: May 2005 Pages: 289 - 298 Strategies for efficient production of heterologous proteins in Escherichia coli S. Jana1 and J. K. Deb
Codon usage
There is a bias in codon usage resulting in variation in translation speed/efficiency. The bias itself varies between organisms (i.e. it is strong in yeast, then in E.coli, much weaker in B.subtilis).
- codon usage database [9]
- graphical codon usage analysis http://gcua.schoedl.de/
One can calculate a number of codon bias indexes using programs:
- CodonW web server, Sourceforge project
- E-CAI HTML "The E-CAI server provides a direct threshold value for discerning whether the differences in CAI are statistically significant or whether they are merely artifacts that arise from internal biases in the G+C composition and/or amino acid composition of the query sequences."
The Vienna RNA package has solutions for many classical RNA problems. It well worth taking some time to familiarize oneself with the algorithms in this package before checking out the alternative methods.
Secondary structure prediction
For Wikiomics:RNA secondary structure prediction from a single sequence the most commonly used tools are MFold and RNAfold. For more single sequence and other comparative methods a large range of methods are available.
For the best accuracy (and evolutionary information) comparative approaches, in particular the alignment folding methods, have proven rather successful. Typically a researcher will align sequences using tools such as ClustalW, MAFFT and ProAlign and then fold the alignment using tools such as RNAalifold or Pfold.
RNA homology search
For the Wikiomics:RNA homology search problem (including secondary structure) a number of algorithms exist. E.g. Infernal and RaveNnA. A number of tools specializing in a specific RNA family are also available eg. tRNA, miRNA etc.
RNA gene-finding
Tools for Wikiomics:RNA gene-finding usually use as input sequence alignmments which are then scanned for potential conserved secondary structure signals. Useful examples of these are QRNA, RNAz and EvoFold.
RNA databases
A number of Wikiomics:RNA databases are available.
- microRNA database (sequences, targets, sumbmission for publications)
- Rfam a large collection of multiple sequence alignments and covariance models covering many common non-coding RNA families.
- BRaliBase Benchmarks of RNA analysis tools on trusted ncRNA datasets.
Protein Alignment
See also article in wikipedia: Sequence alignment software
Two sequences
There are two kinds of alignment: local and global.
- Local
- finds the best region of similarity between two sequences
- water (Emboss) uses the Smith-Waterman algorithm (modified for speed) web interface
- lalign Huang and Miller algorithm [10]
- blast2 [11]
- bestfit (GCG) Smith-Waterman algorithm
- Global
- covers the whole length of both sequences
- needle (Emboss) Needleman-Wunsch global alignment [12]
- gap (GCG) Needleman-Wunsch global alignment
Multiple sequences
For a recent review see Notredame 2007 @PLOS
There is a trade off between accuracy and speed. For speed select MUSCLE. Accuracy of algorithms differs, with the best results on average being achieved using PRALINE and t-coffee/M-coffee. For poteins with multiple/repeated domains you may try graph based algorithms: poa or aba.
- t_coffee (good at producing alignments of distant (~30% similarity) sequences. [13]
t_coffee your_fasta_file.fa
T-Coffee has a limit of 50 sequences. The new version is called M-Coffee, it is a meta-aligner using output of several other algorithms (ClustalW, Poa, Muscle, ProbCons, MAFFT, Dialign-T, PCMA). To run it (bash):
export POA_DIR=/absolute/path/to/Poa/installation/directory export DIALIGNT_DIR=/absolute/path/to/DIALIGN-T/conf t_coffee your_fasta_file.fa -special_mode mcoffee
- MAFFT one of the top alignment programs, with multiple options. See benchmarks from 2006 papers here
- PRALINE (slow but takes into account blast results) [14]
Uses PSI-BLAST for finding most conserved residues in each of the sequences. Very slow but could be more accurate as compared with other methods.
- clustalw (standard algorithm most commonly used and "good enough" in most cases) [15]
clustalw your_fasta_file.fa
output as aln format
- dialign (good for creating alignments with long gaps as with non-orthologues sharing domains only) [16]
Improved, command line version is DIALIGN-T [17]
dialign-t ./path/to/dialign-t/conf/ your_fasta_file.fa your_fasta_file.dialign-t
output is in fasta format
- MUSCLE http://www.ebi.ac.uk/muscle/
muscle -clw -in your_fasta_file.fa -out your_fasta_file.aln -clw
- probcons http://probcons.stanford.edu/
probcons -clustalw -ir 100 -pre 20 -a your_sequence_in_fasta_format.fa > probcons.aln
Graph based algorithm replacing columns with directed acyclic graph. Permits domain recombinations of domains/exons: useful for the alignment of multidomain proteins and ESTs.
poa -read_fasta your_fasta_file.fa -clustal output_file.aln /path/to/similarity/matrix/i.e/blosum80.mat
Method using A-Bruijn graph. Good for alignment of proteins with:
- domains that are not present in all proteins
- domains that are present in different orders in different proteins
- domains that are present in multiple copies in some proteins
DNA: ABA is useful in the alignment of genomic sequences that contain duplications and inversions. Based on: http://www.genome.org/cgi/content/abstract/14/11/2336
- MEME (good for finding as-yet-unknown domains in a set of proteins) MEME web site
meme -nmotifs numberof_motifs_2_find -model oops -protein -sequence your_fasta_file.fa.fa -outfile your_fasta_file.fa.fa.meme
Where 'model' could be oops/zoops/anr.
oops: One Occurrence Per Sequence
zoops: Zero or One Occurrence Per Sequence
anr: Any Number of Repetitions
MEME syntax (see more at http://meme.nbcr.net/meme4_3_0/documentation.html):
meme your_input_fasta_file.fas -nmotifs 20 -mod anr -dna > your_meme_output.htm &
Alignment accuracy assessment
all alignments have to in aligned fasta format and contain the same sequences in the same order.
Paper: http://nar.oxfordjournals.org/cgi/content/full/33/22/7120
Alignment editors & beautifiers
- Jalview (Java) [18]
good for sequence conversion (ALN, MSF, Fasta,Pfam, PIR, BLC)
- clustalx (PC, Unix) [19]
ALN only
- seaview (Linux) [20]
good for sequence conversion (ALN, MSF, Fasta, Mase, Phylip, Nexus)
- genedoc (PC only) genedoc(PC only) very flexible color schemes
- boxshade (no editing, pretty prints only)
LaTeX package. accepts ALN and MSF formats.
- WAViS web server
- accepts multi FASTA with Clustal, NEXUS, GCG, Phylip conversion
- EPS SVG output
Sequence logos
MSA or matrix
- enoLOGOS (first choice)
- WebLogo (input as Fasta, ALN formats)
(single HMM profile)
(pair-wise HMM profiles)
DNA alignment
coding DNA alignment based on existing protein alignment
This is a method of constructing more accurate DNA alignment for downstream use in phylogenic analyses taking into account coding properties of given DNA sequences.
- PAL2NAL webserver capable of dealing with stop codons7frame shifts, suitable also for pseudogenes
- transAlign Perl script, requires Clustalw article
- RevTrans
- protal2dna
- CodonAlign stand alone program
Genomic DNA against genomic DNA
- MUMmer
- PipMaker aligns two DNA sequences
- MultiPipMaker (web server) article Aligns 2-30 DNA sequences
GATA: a graphic alignment tool for comparative sequence analysis
- AuberGene stand alone Python scripts. Requires blastz for pairs comparison.
- SeqAn::T-Coffee multiple sequence alignment program. SeqAn::T-Coffee aligns amino acid, DNA and RNA sequences using a consistency-based progressive alignment algorithm on a graph of sequence segments.
Non-coding DNA sequences
- Sigma [21]
Designed specially for non-coding DNA sequence Paper: [22]
Similarity plots (dot-plots)
For the explanation how it works look here
- dotter(Unix, PC)
Create dot-plots (DNA-DNA, protein-protein and DNA-protein) between one or more sequences. Ideal for quick estimation of sequence similarity, gene organization (genomic DNA vs cDNA), domain finding for small/medium size sequences. One can also zoom an area of interest. Memory and CPU is the limit but one can compare 200kbp genomic DNA vs 6kbp cDNA in ca 2min on 2GHz Pentium 4.
dotter first_fasta_DNA.seq second_fasta_DNA.seq dotter first_fasta_AA.seq second_fasta_AA.seq dotter first_fasta_DNA.seq second_fasta_AA.seq
Note that the order of DNA vs protein comparison matters. Try to keep sequence names within your multiple_fasta file short.
Scaling down image 10x with -z option:
dotter first_fasta_DNA.seq second_fasta_DNA.seq -z 10
Detailed description how to add annotation to dotplots:
The example format of sequence features file (passed with -f option to dotter)
100 @1 CDS 1 1124 RED gene1 100 @1 CDS 3360 3965 RED gene2 100 @1 CDS 3360 3968 RED gene3
- dottup info (Emboss, Unix/Web) web form
- Gepard bacterial genome scale fast dotplots (Java)
Database searches (sequence similarity)
There is a tradeoff between finding all possible matches (like with Smith-Waterman) and speed. For most applications Blast (and Psi-Blast) is a first choice. For massive searches, where speed is essential (i.e. mapping all cDNAs to a mammalian genome) use blat
Regular expressions
Searches for short motifs, like [MC]-A-x-E(2)-{IE} (M or C followed by A followed by any followed by EE followed by anything but I or E)
- fuzznuc (from Emboss)
search nucleotide searches
fuzznuc -sequence your_sequence_for_searching.fasta -pattern 'GATTACCA' -mismatch number_of_mismatches_allowed -outfile output_file.txt
- fuzzpro(from Emboss)
search protein sequences
fuzzpro -sequence your_sequence_for_searching.fasta -pattern 'MEGGADE' -mismatch number_of_mismatches_allowed -outfile output_file.txt
- dreg (from Emboss)-
Regular expression search of a nucleotide sequence
dreg -sequence your_sequence_for_searching.fasta -pattern '[CG](5)TG{A}N(1,5)C' -mismatch number_of_mismatches_allowed -outfile output_file.txt
- preg (from Emboss)
Regular expression search of a protein sequence
preg -sequence your_sequence_for_searching.fasta -pattern '[MARE](2)YDY{AGWK}' -mismatch number_of_mismatches_allowed -outfile output_file.txt
For more help about options/switches in Emboss programs type:
program_name -help -verbose
- ScanProsite [24]
corresponds to:
[C or G] (five times), T, G, {anything except A},1-5 of any, C
More about pattern syntax: [25]
First tier algorithms
- Blast [26]
For the detailed BLAST tutorial see Wikiomics:BLAST_tutorial
Warning: There is a major change of blast standalone binaries. Info below is describing blastall based programs. While most of the options will work with new blast+ , check the information here
Command line: check first if $BLASTDB and $BLASTMAT are set (it should display these names sans $ signs & pathways):
env | grep BLAST
If you get a blank and these are not set in your '~/.ncbirc' file (tcsh):
setenv $BLASTDB /path/to/directory/with/blast/databases/ setenv $BLASTMAT /path/to/your/director/blast/data
or follow instructions for creating '~/.ncbirc' from here: [27]
to create a database out of your fasta file:
formatdb -i your_multiple_protein_file.fa -p T -V formatdb -i your_multiple_DNAseq_file.fa -p F -V
For more options type 'formatdb -h'
- nucleotide search
blastall -p blastn -d ecoli_nn -i my_nn_fasta_file.fa -o my_nn_fasta_file_vs_ecolidb.blastn_out
- protein search
blastall -p blastp -d ecoli_aa -i my_nn_fasta_file.fa -o my_nn_fasta_file_vs_ecolidb.blastp_out
- Blast2 [28]
finding similarity between two sequences/alignment + dotplot on the web f
comparing protein sequence with DNA:
bl2seq -p tblastn -F N -i your_peptide_sequence.fasta -j your_nucleotide_sequence.fasta
- Blat
- description: http://www.genome.org/cgi/content/full/12/4/656
- web server: http://genome.ucsc.edu/cgi-bin/hgBlat?command=start
- command line
blat /path/to/database your_query_in_fasta.fa [-ooc=11.ooc] output.psl
-ooc=11.ooc option speeds up search by using a set of over-occuring 11-mers to create your database out of DNA sequence file:
faToTwoBit input_fasta.fa [in2.fa in3.fa ...] output.2bit
use output.2bit as a database in your blat searches.
Slower but more sensitive
- FastA [29]
- Smith-Waterman/MPsrch [30]
- only Protien queries. Emboss water [31] can be used to search local nucleotide databases .
- Scanps (SW variant) [32]
HMM and profile searches
- HMM searches
- hmmer [33]
hmmbuild your_ALIGNED_sequences.hmm your_ALIGNED_sequences.fasta hmmcalibrate your_ALIGNED_sequences.hmm hmmsearch your_ALIGNED_sequences.hmm protein_database.fasta
in HMMER3 you have to specify the format, i.e.
/hmmbuild --amino --informat afa --cpu 8 your_ALIGNED_sequences.hmm your_ALIGNED_sequences.fasta
- MEME MAST [ http://meme.sdsc.edu/]
Command line:
mast your_meme_motifs.meme -d your_database.multiple_fasta
Data mining
finding basic info about known gene
$$$ very preliminary at the moment $$$
- select a set of sequences
- create alignment
- remove bad regions of the alignment/gaps (tree constructing programs deal badly with indels)
- for more than 12 sequences tha space of all possible tree is to large to search one-by-one -> heuristic methods are used
- maximum parsimony MP
sensitive to the order of sequences.
- distance methods
- Neighbor joining NJ
- UPGMA (Unweighted Pair Group Method with Arithmetic mean) assumes rate of mutation constant along branches of a tree. Less accurate for sequence data than NJ.
- maximum likehood (computationally intense, but more accurate)
To check validity of a tree:
- bootstrap
After creating a tree from MSA bootstrapping program selects number of columns from MSA and calculates a tree. This process is repeated 100-1000 times and resulting trees are compared with previously created one. Branches present in more than 70% of bootstrap samples are believed to have a good support. These estimates are conservative
- multiple samples from the posterior distribution (MrBayes)
Probably overestimate confidence values [38]
- PHYLYP (phylogeny standard package) see a guide to it: [39]
Individual programs can be scripted. On unix (bash):
- create a new directory
- put your_aligned_proteins.phylip there
- start any text editor, modify content below to suit your options, save as i.e. run_proml_with_my_options.sh
#!/usr/bin/sh proml << EOF your_aligned_proteins.phylip 1 S y EOF
- run it
source run_proml_with_my_options.sh
- after completein the run it reports:
Output written to file "outfile" Tree also written onto file "outtree"
- PHYML http://atgc.lirmm.fr/phyml/ (ML)
- MrBayes http://mrbayes.csit.fsu.edu/ (Bayes / Markov chain Monte Carlo.)
requires NEXUS format. To tun it on command line: 'mb'
- RAxML-VI http://www.ics.forth.gr/~stamatak/index-Dateien/Page443.htm (ML for large phylogenetic trees)
- TREE-PUZZLE http://www.tree-puzzle.de/ (ML)
- Mesquite collection of modules for performing a wide range of analyses from various branches of evolutionary biology (e.g., phylogenetics, molecular evolution, population genetics, geometric morphometrics)
Molecular clock
- BEAST (Linux, Win, Mac) Bayesian MCMC analysis of molecular sequences
Tree display
For the comprehensive list see: http://en.wikipedia.org/wiki/List_of_phylogenetic_tree_visualization_software
- PhyloWidget novel (2008) program (standalone + web java widget)
- extensive list of programs: http://evolution.genetics.washington.edu/phylip/software.html
- tutorial articles:
Genomic structure
One gene in one species
Almost 20 species have as for today (May 2006) separate entries in Ensembl. Possible searches include: blast, GeneBank accession number, gene symbol, chromosomal band, marker etc. To elucidate genomic organization (exons/introns) of a gene starting from a known gene name/accession number.
- Ensembl (known transcript)
- go to Ensembl
- click on a link to an organism of interest say Human (Homo sapiens)
- on the top of the page, "Search for:" (select "Gene" from pull down menu)
- put the gene symbol (i.e. p53), Search
- select from the list of hits Ensembl gene (click on the red link)
- you are in "Ensembl Gene Report"
- right to "Sequence Markup" click on " View genomic sequence for this gene with exons highlighted"
- the sequence (including SNPs) is displayed
- Spidey (novel transcript)
- get cDNA sequence in FASTA format
- check it for repetitive sequences using RepeatMasker
- get genomic sequence containing the gene with 1-10kb flanks
- check the gene structure using dotter this is to detect cDNA/genomic DNA miss-assembly/gaps etc.
- go to http://www.ncbi.nlm.nih.gov/IEB/Research/Ostell/Spidey/spideyweb.cgi
- fill in the form selecting the proper splice site matrix (so far: vertebrates, Drosophila, C. elegans, or plants)
- you get a table with genomic coordinates/mRNA coordinates, exon length, % of identity, number ofmismatches, gaps, precence or abcence of splice donor and acceptor sites
Very good at finding exons in the same species (i.e human cDNA/human genomic sequence), more problematic with cross-species comparisons (i.e. human cDNA, bovine genomic sequence -> most of the exons OK, with few bad predictions).
comand line only. Slow but good at finding small exons. So far has matrices for human (default), mouse, rice and C.elegans.
exalin your_genomic_sequence.fa your_cDNA_sequence.fa
- wise2 [40]
Best for: comparing a protein sequence or hmm profile to a genomic/cDNA sequence from other organism Restrictions: fasta headers longer than 15 characters are truncated
One needs to set up env variable for wise, i.e bash:
export WISECONFIGDIR=/usr/biosoft/packages/wise/wise2.2.3-rc7//wisecfg/
- peptide vs genomic DNA:
genewise your_peptide_sequence.single_fasta your_genomic_sequence.single_fasta
- HMM profile vs genomic DNA:
genewise -hmmer your_hmm_profile.HMM your_genomic_sequence.single_fasta
- peptide vs cDNA/EST
estwise your_peptide_sequence.single_fasta your_cDNA_sequence.single_fasta
- HMM profile vs cDNA/EST
estwise -hmmer your_hmm_profile.HMM your_cDNA_sequence.single_fasta
- GeneSeqer WWW server + stand alone program. Multiple species models.
- Pairagon [41]
standalone cDNA-to-genome alignment program
- PALMA 2007 program stand alone claimed to outperform other algorithms. Parameter files for human, C.elegans, arabidopsis and drosophila (Nov 2007)
One gene in multiple species
Structured Visualization of Evolutionary Conserved Sequences. Provides colorful graphs depicting intron exon orientation with sizes.
- go to SVC
- put gene symbol (i.e. SYNGR3) or better Ensembl ID (i.e. ENSG00000127561) into 'Input ID'
- check species of interest in 'Search for orthologs in:'
- Click 'Submit' next to 'Input ID'
Bacterial genomics
- SEED precomputed similarities, annotations using colocalization in operons. Very efective for annotation new genes.
- Integr8 Ensembl-like interface to bacterial genomes
- WebACT WebACT genome-2-genome comparisons
Promoter prediction
Predicting promoters based on a single sequence is rather unaccurate. Transcription factor (TF) recognition sequences are fairly short, therefore any sequence 1kbp in lenght will contain hundreds of such motifs, only a handful of which will be a true positives. There are two major methods used for finding relevant sites
- phylogenetic fingerprinting (comparison of promoter regions between orthologues)
- comparison of promoter regions of genes with similar expression profiles in the same species
We can look for either known TFs recognition sequences (quality of which depends on database used) or perform motif finding de novo, looking simply for any streach of DNA shared between species/co-expressed genes.
- before you start
make sure that you got a real 5' end exon of the gene (a lot of longer genes in the databases may be missing the true 5'end). You verify quality of your gene of interest by:
- comparing with orthologues ( Ensembl or Homologene) If close orhologues are longer on the protein level, look for the presumptive missing exon(s).
- looking at the genomic context (other genes flanking yours)
- blasting cDNAs 5' end against ESTs database looking for any ESTs extending your gene
- blasting masked genomic sequence, from 5' end exon to the start/end of the flanking gene
Interpretation of this one may be tricky, on the simplest level look for spliced matches with ORFs in the same orientation as your gene without clear stop codons.
- find position of repeats
After checking the 5' end of the gene, always look for repetitive sequences using RepeatMasker. It does not mean that say Alu/LINE1 can not be a part of the promoter. Just that you may concentrate on parts which are a bit more specific for the given gene.
phylogenetic fingerprinting
comparisons of promoter regions of orthologous genes in other species
- obtain these using Ensembl [42]
- use tools described below to find out shared TF binding sites/comon motifs
- comparing closely related genomic sequences (human and chimp) is not stringent enough
- comparing wildely different sequences (human and zebrafish) is too stringent for all but small set of genes (i.e. homeobox?)
comparing promoters of coexpressed genes in the same species
- use GEO (Gene Expression Omnibus) [43] to find gene(s) with simmilar expression
- get promoter sequences using Ensembl [44]
Quality depends on the underlying database of TF binding sites
- Consite produces a set of transcription factors binding sites shared between two sequences
- zpicture plus rVISTA
- Conreal (multiple alignment algorithms) [45]
- Confac [46]
- Mulan multiple sequences
- Footprinter [47]
For more in depth coverage see: Wikiomics:Sequence_motifs
This method will work even for unknown TF binding sites, but it may skip some more degenerate motifs.
- MEME capable of discovering longer motifs, very sensitive
- Improbizer takes into account position of the motifs
- AlignACE Gibbs sampling algorithm
- MDscan
It is important to use few complementary programs as well as allow predictions of several motifs per program. There is threshold when it comes to number of sequences used, above which there is no improvement in sensitivity.
Comparison of several programs: http://nar.oxfordjournals.org/cgi/content/full/33/15/4899#TBL1
Promoter Databases
- Eukaryotic Promoter Database
- Mammalian Promoter Database MPromDb
- DoOP eukaryotic promoter sequences
- DBTSS Database of Transcriptional Start Sites
Transcription Factiors Databases
- JASPAR (open transcription factors database)
- TESS(finding transcription factor binding sites within your sequence)
Be aware that simply listing all recognizable TF binding sites in a given stretch of DNA is almost of no value. Only 0.1% of the putative sites listed that way will be functional (Applied bioinformatics for the identification of regulatory elements WW Wasserman, A Sandelin - Nature Reviews Genetics, 2004)
Reviews & tutorials
- gene regulation tools site very comprehensive
- Other tutorial (you need an access to Nature Immunology): [48]
- PLOS Apr 2006 MacIsaac and Fraenkel article [49]
- For an extensive table of known programs used for finding motifs see [50]
Transcription start finding
There are various clases of such programs starting with completa ab initio promoter finding using genomic sequence only, through combining it with ab initio gene fining, finally taking into account ESTs data and/or gene annotations. Most of the programs were evaluated on human or mammalian sequences and may not be suitable for other groups of organisms. Masking repeats using RepeatMasker improves performance of McPromoter(strongly) and FirstEF (mildly), whereas has no effect on Eponine and DragonGSF.
- N-SCAN (standalone only derivative of TwinSCAN) [51]
- Eponine (mammalian) [52]
- FirstEF (human) [53]
- DragonGSF [54]
- McPromoter (fly, with older version for human) [55]
- PromH (promoters identification using orthologous genomic sequences) [56]
- VISTA Enhancer Browser Human/vertebrates enhancers DB
- Bajic et al. Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment
Genome Biology August 2006 [58]
- Bajic VB, Tan SL, Suzuki Y, Sugano S: Promoter prediction analysis on the whole human genome. Nat Biotechnol 2004, [59]
SNPs (Single Nucleotide Polymorphism)
- NCBI SNP database http://www.ncbi.nlm.nih.gov/SNP/ (strongly recommended)
- HGVbase Phenotype/Genotype database (funding expired?)
- JSNP http://snp.ims.u-tokyo.ac.jp/ (some access problems)
- CSHL http://snp.cshl.org/
Gene expression
- go to Unigene (ESTs derived from the gene)
- search Unigene with gene symbol (i.e SYNGR1) or Unigene cluster (i.e. SYNGR1)
- look at Expression and distribution of ESTs [60]
- click on Expression profile to see electronic Northern
Wide array of tissues and genes.
- go to Symatlas
- put your gene symbol, i.e. SYNGR1
- click on a small icon left to human or mouse genes
in situ hybridisation images
- Gensat
Atlas of in situ hybridization of mouse brain
- Genepaint
Atlas of in situ hybridization in mouse embryos. One can order hybridization of a gene of interest.
Digital Differential Display
Searching info about gene homologues in other databases
- Mouse [61]
- C.elegans & co. [62]
- D. melanogaster [63]
- S. cerevisiae SGD@stanford [64]
- Proteome (multiple organisms) [65] ($$$) (databases of S. cerevisiae, S.pombe and WormPB [C.elegans+]
Finding protein domains
Finding protein motifs
Disulfide bond predictions
- DISULFIND Newest
Sequence/structure retrieval
- Entrez
- Batch Entrez (retrieving multiple DNA/protein entries at once):
- SRS (complex queries )
- PROMPT Protein Mapping and Comparison Tool
Protein localization and structure prediction
- collection of links: [66]
- TarO queries multiple servers
Start with:
- Evaluating eukaryotic secreted protein prediction [67]
- Localizome server Localizome combines prediction of Phobius, Pfam, LocaloDom (database of TM topologies and TM helix numbers of around 3,000 eukaryotic Pfam domains)
- The maximum number of input proteins in a single submission is 500 protein.
- The length of each sequence is limited to 6,000 residues.
Standard choices
In evaluation (localization):=
- MultiLoc
- LOCSVMPSI (localization, results by email) site down 2010-03-11
- BaCelLo (max five fasta sequences)
- ProteinProwler (plant/nonplant and four localizations only)
- Recent review: Punta, Marco, Lucy R. Forrest, Henry Bigelow, Andrew Kernytsky, Jinfeng Liu, and Burkhard Rost. "Membrane protein prediction methods." Methods 41, no. 4 (April 2007): 460-474.
- top servers were evaluated by Cuthbertson et al.( Protein Engineering Design and Selection 2005) full text:
- Other servers:
- ConPred2 Consensus TM prediction (metaserver)
- Phobius (includes signal peptide predictions)
- PRODIV-TMHMM ref: [68] (results send by email, prediction of TM topology)
- MemBrain (includes signal peptide predictions) claims to outperform several other top scoring TM predicting programs paper(HTML)
see also links here: [69] and the Signal Peptide section
signal peptides
- SignalP
- Phobius (predicts signal peptide, TM and orientation)
- PolyPhobius Homology supported signal peptide predictions
Accepts both single fasts seqence as well as aligned sequences in multiple fasta format (only the top sequence appears in the output).
- Phobius author PhD thesis: [70]
Other Programs:
- SPEPlip Eukaryots/Prokaryots
- TatP Twin-arginine signal peptide cleavage sites in bacteria Paper: [71]
- LipoP lipoprotein signal peptides in Gram-negative bacteria. Paper: [72]
protein structure (no-3D)
- Expasy [73]
- Coils (coiled coil prediction) [74]
- Protscale (various prediction based on AA sequence) [75]
- Jpred (multiple secondary structure predictions run in parallel) [76]
Graphical plots of protein 2D structure
- TMRPres2D standalone Java program. Top choice:
' 'One-step' data input procedure, including easy querying of the public databases and incorporation of output from various popular prediction tools available from the Web.' allows creating graphs with transmembrane regions, signal peptides, disulfide-bridhes, glicosylated residues etc.
- TOPO2 web based
Protein structure databases/comparisons
Metabolic networks
$$ needs more work$$
- Reactome
- BioCyc
- Cyclone - provides an open source Java API for easier access to BioCyc.
- RegulonDB E.coli K12 DB (operons/genes/regulatory elements)
Protein-protein interactions
Large scale methods such as yeast-two-hybrids (Y2H), immuno-co-precipiatation (IP) produce a large number of false positives. Only about 30-50% of interactions seem to be relevant. While newer improvements of these procedures tend to be more accurate, existing databases struggle to separate good quality data.
- IntAct@EBI literature and user submission data.
- BindingDB
- BioGRID
- Mammalian Protein-Protein Interaction Database @MIPS
- STITCH Chemical-Protein Interactions
Restricted access ($$$ ?):
- BIND / BONDplus (registration required)
- APID Agile Protein Interaction DataAnalyzer
Where to find more information
- Bioinformatics Links Directory @UBiC
- Approaches to Web Development for Bioinformatics
- Bioinformatics Resources - Medical Computing .Net
Also there are relevant pages on Wikiomics web site:
- Darek Kedra wrote this tutorial


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All data and information provided on this site is for informational purposes only. The Office Dynamics Blog makes no representations as to accuracy, completeness, currentness, suitability, or validity of any information on this site and will not be liable for any errors, omissions, or delays in this information or any losses, injuries, or damages arising from its display or use. All information is provided on an as-is basis.


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Download and listen to each Keynote from FOCUS Conference 2011 right to your computer.
Beyond Boredom by Christopher Stefanick
Answering The Call by Curtis Martin
Waking The Sleeping Giant - How Discovering Our Gifts Will Renew the Church by Jeremy Rivera
Chicks, Liquor, Drugs: God is Calling, But I'm Not Answering Cuz I Think He's a Telemarketer by John Leyendecker
Equipped For Mission by Jonathan Reyes, Ph.D
Passionately Loving the World : It's Everyones Call to Build a Culture of Life by Lila Rose
Blazing a Trail of Glory by Sr. Mary Gabriel, S.V.
Behold I Make All Things New: Living the Confidence of the Saints by Sr. Mary Gabriel, S.V.
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The Salome Set is one of our favorites! The outfit features a spotted bodysuit, spice-colored shorts with bow in front and matching ginger-colored bow headband.
⋒Material: 100% Cotton
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⋒Fits true to size, if your child is between sizes we recommend sizing up
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If you have any questions or concerns regarding your order, please reach out to us at email@example.com
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We now use Shopify Markets which is a program that allows us to include import duties & tax at checkout so there are no additional charges when you receive your order. There are times when an international order can be subject to additional import duties & tax when your package arrives to its destination. This instance will vary from country to country, please get in contact with your local customs office for more details.
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this item is true to size, for a relaxed fit we recommend going up 1 size
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text:
In 2007, YouTube launched a more advanced Flash-based video editor called YouTube Remixer, but it was discontinued. The service was based on Adobe Premiere Express and, despite offering features like transitions, captions, adding images, it was slow and buggy.
Here are some videos created using YouTube's new video editor.
{ Thanks, Kevin. }


text:
"Customer selection and profit maximization in vehicle routing problems",
Operations Research Proceedings 2005: Springer Berlin Heidelberg, pp. 37–42, 2006.
"A Matheuristic for Leader-Follower Games Involving Facility Location-Protection-Interdiction Decisions",
Metaheuristics for Bi-level Optimization: Springer Berlin Heidelberg, pp. 115–151, 2013.
"Open vehicle routing problem with time deadlines: Solution methods and an application",
Operations Research Proceedings 2005: Springer Berlin Heidelberg, pp. 73–78, 2006.
"Location and selective routing problem with pricing for the collection of used products",
Computers and Industrial Engineering (CIE), 2010 40th International Conference on: IEEE, pp. 1–6, 2010.
"A bilevel fixed charge location model for facilities under imminent attack",
Computers & Operations Research, vol. 39, no. 7: Pergamon, pp. 1364–1381, 2012.
"A bilevel partial interdiction problem with capacitated facilities and demand outsourcing",
Computers & Operations Research, vol. 41: Pergamon, pp. 346–358, 2014.
"A bilevel p-median model for the planning and protection of critical facilities",
Journal of Heuristics, vol. 19, no. 2: Springer US, pp. 373–398, 2013.
"The budget constrained r-interdiction median problem with capacity expansion",
Central European Journal of Operations Research, vol. 18, no. 3: Springer-Verlag, pp. 269–291, 2010.
"Design and analysis of government subsidized collection systems for incentive-dependent returns",
International Journal of Production Economics, vol. 119, no. 2: Elsevier, pp. 308–327, 2009.
"Locating collection centers for distance-and incentive-dependent returns",
International Journal of Production Economics, vol. 111, no. 2: Elsevier, pp. 316–333, 2008.
"Locating collection centers for incentive-dependent returns under a pick-up policy with capacitated vehicles",
European Journal of Operational Research, vol. 191, no. 3: Elsevier, pp. 1223–1240, 2008.
"The r-interdiction selective multi-depot vehicle routing problem",
International Transactions in Operational Research, vol. 27, pp. 835-866, 2020.
"Selective multi-depot vehicle routing problem with pricing",
Transportation Research Part C: Emerging Technologies, vol. 19, no. 5: Elsevier, pp. 866–884, 2011.
"A trilevel r-interdiction selective multi-depot vehicle routing problem with depot protection",
Computers & operations research, vol. 123, pp. 104996, 2020.


text:
Macher Paturi |
The word "paaturi" comes from the Bangla word "paata" or leaf . That said, it becomes crystal clear that "Maacher Paturi" or Fish Paturi is a preparation where the fish is cooked in some sort of a leaf.
It being a Bengali recipe. it also becomes more than crystal clear that the said fish has been marinated in a sharp, pungent mustard-y paste of shorshe bata and drizzled with mustard oil. Okay, apparently there is a non-Ghoti version where the fish is wrapped in other spice pastes, not necessarily mustard but I have not tried that.
Once these two bases have been covered you are free to "go as you like" on Maachher paturi.
More than 20-25 years ago,
1. The maacher paturi that I would eat would always be prepared by my Dida.
2. The fish would always be Ilish.
3. The leaf would always be Banana. Some homes do their paturi in gourd leaves like Lau Pata and they taste very good too.
Kolapata was easily available, an arm's length away, growing in perfect neglect amongst the jackfruit and pampered mangoes, making it the leaf of choice. Dida would dab the fresh Ilish pieces with shorshe bata and kaancha shorsher tel, throw in a few green chillies and wrap them up in cut rectangular pieces of the Banana leaf. With an expert hand she then neatly tied the fish parcels with twine, an act which I looked at with much wonder. Not being a very dexterous kind myself, I found the whole "tying with twine" part a very complex act and based on that memory of neat parcels alone, I labeled paturi as a dish difficult to concoct.
Once the parcels were ready, Dida would tuck them into the steaming rice, that was cooking in a large pot on the coal stove. This tucking would happen towards the very end of the rice cooking and the latent heat from the hot rice would steam the fish in their banana leaf parcels. When those leafy envelopes were opened to reveal the mustardy fish, the fragrance was ethereal. Have you ever taken a strong whiff of banana leaf that has been warmed with steaming rice and then spiked with aroma of shorsher tel and Ilish ? It is hard to describe. Just like it is hard to explain the fragrance of tea in earthen kulhars or the perfume of yellow stalked sheuli that has touched the wet earth on autumn mornings.
Some days Dida would also tuck those leafy fish parcels in the dying embers of the unoon or coal stove. The fish cooked slowly, soaking up the flickering heat and smoke, while Dida cleaned up the kitchen, took a shower and offered white balls of nokuldana to her Gopal. That Paaturi tasted a little different from the one cooked in steaming rice. Here the kolapata was lightly charred and had a smoky fragrance where in the other the flavor was more clean and dominated with the fragrance of rice.
20 plus years later, the paturi that I make has the new woman's twist on it. The fragrance is not exactly as it would be in Dida's kitchen.
1. The Banana leaf is bought frozen, in exchange of several dollars from an Asian Store.
2. The fish is not always Ilish and fillet of fish like Swai, Salmon and Tilapia are abundantly used.
3. Instead of tucking the fish parcels in a pot of steaming rice or in dying embers, I just put them in the oven.
4. And oh, I never use twine to tie them up. I use toothpicks to secure the packets and heave a sigh of relief.
But the taste is pretty close. The fish cooked in the banana leaf, is delicate and flavorful, the mustard paste is just as sharp and pungent, the fragrance of the banana leaf as ethereal.
Some things never change.
You can also steam them in a steamer like this or do them over a covered griddle on the stove. But I almost always do it in the oven, because that way I can forget about them while they cook on timer and go about my life of getting homework done, folding the laundry and prepping for next day's lunch.
When it is dinner time, "ting-ting" there is delicious paturi to be had. Amazingly I had blogged about a Thai Fish wrapped in Banana leaves a couple of months ago and given a choice between the Bengali fish paturi and Thai fish in banana leaf, it is hard for us to choose. We love both equally.
Clean the fish and get it ready. If you are using fish fillet cut each fillet in about 3"x 3" pieceI started with 2 fillet of swai, each cut in 3.
Make homemade Kashundi. The best option and that Kashundi will serve many purpose.
If you are reluctant to do so make Mustard Paste as follows:
Soak 3 tbsp of Mustard seeds + 1 tsp Poppy seeds in water for 20 minutes
Drain and put in a blender jar along with 4-5 hot green chillies.
With a splash of water make a thick paste.
Now if I am using fish other than Ilish/Hilsa, I also add 2 cloves of garlic to the blender jar and make a garlicky-mustard paste
In a bowl, pour the
mustard paste
1 tbsp Mustard oil
salt to taste
pinch of turmeric powder
Mix and make a smooth paste.
Variations: Sometimes with mild fish that does not have much flavor of its own like Swai etc., I add some more things to the mustard paste. Like I add couple of tablespoons of dhonepata chaatni(coriander chutney) to the mustard paste and then use it as the marinade. Try it. Mustard with fresh coriander adds a beautiful layer of flavor.
If you have bought frozen banana leaves, defrost them first by keeping them out at room temperature. Then cut them in rectangles of 6" x 6" or your preferred size. Wash each piece. Dry. Keep aside.
Now I buy frozen banana leaves which are already wilted and perfect for wrapping.But if you have fresh banana leaves, you need to prep them for wrapping. First cut off the central thick rib and trim the edges. Then cut them in preferred size. To make them flexible you need to wilt them. For that pop them in the oven at 200F for 5-8 minutes or warm them over very low flame of your stove/gas range. Be careful that you do not char or burn them in the process.
Start Cooking
To marinade the fish, you can either use your home-made Kashundi or Mustard paste.
Put the fish fillet on the banana leaf.
Rub with sprinkle of salt (mustard paste already has salt so very little on fish) and smear generously with the mustard paste.
Add few drops of mustard oil.
Garnish with a tbsp of grated coconut and slit and chopped green chilli. If using frozen grated coconut , defrost it before using.
Wrap the banana leaf to make a parcel as shown. Secure the loose ends with a toothpick.
Now usually I let these parcels rest for about 30 minutes before popping them in the oven. For a big party, I make the parcels a day ahead and refrigerate(NOT freezer). And then just an hour before the meal, I take them out and let them sit at the counter. I put them in the oven 25-30 minutes before the meal is to be served. That way you get fresh steaming paaturi with minimal effort on party day.
Put the packets on a oven proof tray. Pre-heat oven to 350F. Bake these fish parcels for 20-25 minutes until you see the banana leaf charring slightly around the edges.
I serve the parcels individually along with steaming white rice.


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The Princeton University Board of Trustees has approved the appointments of seven faculty members, including two full professors and five assistant professors. The trustees also revised the appointment of Assistant Professor of Near Eastern Studies Liora Halperin to be effective July 1, 2012, rather than Sept. 1.
Amitava Bhattacharjee, in astrophysical sciences, joined the faculty effective Aug. 27, 2012, from the University of New Hampshire, where he has been a faculty member since 2003. He previously served as a research fellow at the University of Texas-Austin and taught at Columbia University and the University of Iowa. Bhattacharjee's research focuses on theoretical plasma physics, and his research interests and publications cover magnetic reconnection, turbulence and singularity formation, kinetic theory, free-electron lasers and complex plasmas.
He holds a bachelor's degree from the Indian Institute of Technology, master's degrees from the University of Michigan, and a Ph.D. from Princeton.
Mihalis Dafermos, in mathematics, will join the faculty on Jan. 1, 2013, from the University of Cambridge, where he has taught since 2004. Previously, he was an instructor at the Massachusetts Institute of Technology.
Dafermos specializes in partial general relativity and mathematical physics. His publications include numerous papers on the formation and stability of black holes. Dafermos received his B.A. from Harvard University and his Ph.D. from Princeton.
Assistant professor
The following appointments are for three-year terms:
Emmanuel Abbe, in electrical engineering and applied and computational mathematics, began his term Sept. 1, 2012. Abbe specializes in information theory, and he previously was a postdoctoral fellow at Ecole polytechnique federale de Lausanne, where he received his bachelor's and master's degrees. He holds a Ph.D. from MIT.
Simone Giombi, in physics, joined the faculty on Sept. 1, 2012. Formerly a postdoctoral fellow at Perimeter Institute for Theoretical Physics in Ontario, Giombi's research focuses on high energy theory. He received his B.S. from the University of Bologna and his Ph.D. from Stony Brook University. He previously was a postdoctoral fellow at Harvard.
Michael Mueller, in mechanical and aerospace engineering, began his term on Sept. 1, 2012. A specialist in thermal sciences, Mueller received his B.S. from the University of Texas-Austin and his Ph.D. from Stanford University.
Arvind Narayanan, in computer science, joined the faculty on Sept. 1, 2012. Narayanan's fields of specialization are systems and security, and his previous position was as a postdoctoral fellow at Stanford. He earned bachelor's and master's degrees at the Indian Institute of Technology, Madras, and his Ph.D. at the University of Texas-Austin.
Bridgett vonHoldt, in ecology and evolutionary biology, will begin her term on July 1, 2013. A specialist in evolutionary biology, vonHoldt is a postdoctoral fellow at the University of California-Los Angeles, where she earned her Ph.D. She received her bachelor's degree from Eckerd College and her master's degree from New York University.


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All fuel assemblies - 1331 used and 202 new - in the Spent Fuel Pool of Reactor 4 at Fukushima I Nuclear Power Plant have been moved out of the pool. Most have gone to the Common Pool on the ground level. Some have been moved to the Spent Fuel Pool of Reactor 6, as they ran out of space in the Common Pool.
I suppose the purpose of the whole exercise was to placate those who were screaming "End of the world is near!" because "Reactor 4's building would collapse at any moment!" in various parts of the world (particularly North America). Condolences to workers who had to do the actual work and were exposed to large doses of gamma radiation that came from the operating floor of Reactor 3 right next, and from the Reactor 4 spent fuel pool itself due to the high level of cobalt-60 in the water in the Spent Fuel Pool; the water came from the DSP (device storage pool, where Reactor 4's core shroud had been stored temporarily) when the gate to the SFP was damaged in probably one of the aftershocks after the March 11, 2011 big earthquake and let the DSP water flood into the SFP. I wonder if TEPCO ever decontaminated the pool water.
Riken finally and very bluntly announced that the experiment to "recreate" STAP cells was a failure. Not even the 31-year-old Dr. (for now, till Waseda University, aka "PhD diploma mills" as many say now, revokes her degree) Haruko Obokata, who claims to have created the so-called STAP cells more than 200 times, couldn't do it, not even once. DNA analysis proved that Obokata's novel "STAP" cells were nothing but ES (embryonic stem) cells already known and widely used by reseachers.
Riken also concluded that there was NO EVIDENCE that Obokata had actually done the experiments that were reported in the Nature paper and letter. Everything, most likely, was made up. Outright fraud. I wonder if Harvard University is doing any investigation. After all, the Vacanti (of Vacanti-mouse fame) lab is where Obokata learned the trick.
Dr. Obokata released the statement saying she had "tried beyond my soul," whatever that means. Some accuse her of plagiarizing a famous sumo wrestler's words when he announced his retirement. (It seems to me that Obokata had confessed to her fraud when she said back in June this year that she wanted to be reunited with her "sons". Estranged Sons. ES.)
However, Riken very generously exonerated Obokata by saying they couldn't identify who "mixed in" ES cells more than 200 times.
From Riken's English summary of the detailed report (which is only available in Japanese, for experts and researchers):
It is unlikely that there was accidental contamination by three different ES cells, and it is suspected that the contamination may have occurred artificially. However, given the difficulty of identifying who might have contaminated the cultures, it is not possible to conclusively determine that it was artificial contamination. We cannot, therefore, conclude that there was research misconduct in this instance.
Obokata was allowed to quietly resign. It's good to be very well connected, I suppose, having Prime Minister and Minister of Education as fans.
The US and the West propaganda of Russia being the cause of all ills in the world notwithstanding, this one doesn't seem like being caused by Russia. There is a media report that the largest nuclear power plant in Ukraine and in Europe (and 5th largest in the world) may have a radioactive leak. The source of this news is RT, which has unfortunately not been that reliable when it comes to news about the Fukushima nuclear accident. RT quotes LifeNews that reports leaked official report.
From RT (12/31/2014):
A radioactive leak has been detected at Ukraine's Zaporozhye Nuclear Power Plant, the largest in Europe, a media report says, citing the country's emergency services. Ukrainian officials have denied the report.
LifeNews published what it claims is a leaked report by the State Emergency Service of Ukraine, which denies an earlier assessment by the plant's authorities that the radiation at the facility is equal to the natural background following an incident on Sunday.
RT is trying to verify the report.
Ukrainian authorities have denied the Russian media report that a radioactive leak had taken place at the plant, Reuters reported.
"The plant works normally, there have been no accidents," an energy ministry official told the news agency. No official comment on whether the leaked documents are authentic has been provided.
Two documents released by LifeNews appear to show that the plant's officials put deliberately misleading information on their website. The documents – both addressed to the head of the regional emergency services – state that radiation levels at the plant on Sunday and Monday were 16.8 times higher than the legally permitted norm.
By Monday, the levels had slightly increased – growing from 16.3 to 16.8 times higher, and Unit 6 was still shut down, the report said, contradicting the plant's statements that the problem had been fixed and that the plant was operating normally.
(Full text at the link)
The article also says that the US Westinghouse (Toshiba) will "significantly increase fuel deliveries to Ukrainian nuclear power plants through 2020".
Good luck Ukrainians, if what Russia's Sputnik news agency has been tweeting is true.
From Sputnik (12/30/2014):
Nuclear energy experts and officials have repeatedly warned the Ukrainian authorities that it would be unsafe to use US-made fuel in reactors of Soviet and Russian design.
Happy New Year, everyone. I hope we will somehow survive and thrive in 2015, the year of sheep. (...)


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Good design is inevitable. It's determined. It's relentless. Each iteration builds on the one before, becoming better and better each time. The work of Jonathan Ive, Apple Senior Vice President of Industrial Design, is a near-perfect example of this. So is the iPhone 5.
Ive said as much in an interview with the Telegraph back in May:
You can not like the iPhone 5 design as a matter of personal taste. You can wish it were otherwise, or that Apple had chosen to go in a different direction. If you're "disappointed" in the iPhone 5 however, if you think it's too similar to previous iPhones, if you think Apple isn't innovating "any more", you're wrong. I'm not a "fanboy" and you're not a "troll" or a "hater". You're just wrong.
Back in 2005 Apple had a phone prototype called Purple. It was a flat, rounded rectangle with a big screen on the front and a metal plate on the back. It was, perhaps, their platonic ideal. Their form phone. And they couldn't make it. Not back then. They lacked the mobile engineering experience of an established player like Nokia, and they lacked the technologies and manufacturing processeses they themselves would later develop.
So Ive and Apple were forced to do what all great designers do. They were forced to compromise. And we got the original iPhone with its bloated sides and a big plastic band breaking its aluminium back. For the iPhone 3G and iPhone 3GS, the metal back was removed completely, and plastic, bloated as the sides, took its place.
With the iPhone 4 and iPhone 4S, Ive and Apple were finally able to engineer their Purple phone. Flat. Solid. Stainless steel. But glass on the back and still not metal, and with an exposed antenna array that took a generation to get right.
Now we have the iPhone 5. Another step closer to Purple, the stainless steel sides are replaced by aluminium and the metal plate on the back has finally returned, albeit not completely. Another set of compromises demanded they keep radio-friendly glass on the top and bottom, and Apple's choice in a wider screen has forced them to abandon their golden ratio.
Master your iPhone in minutes
iMore offers spot-on advice and guidance from our team of experts, with decades of Apple device experience to lean on. Learn more with iMore!
Jony Ive has many times said his goal is nothing less than making a better product. Phil Schiller said as much yesterday as well -- they started with the idea of an iPhone that was 20% or more thinner and lighter than an iPhone 4S without sacrificing any battery life, camera optics, or screen quality. And they did it while improving all of those things, and adding a faster radio as well.
Lost amongst the angst and howls of those for whom design is an appearance thing -- for whom ever more giant, creaky, plastic phones that are gray one year and blue the next, that are thin on one end and humped on the other, that sacrifice pixel quality for size, and consistency and cohesiveness for feature creep, are innovation -- is the leap forward Ive and Apple are taking here.
The leap from iPhone 4S to iPhone 5 is no less significant or impressive than the leap from the original MacBook Pro to the Unibody. In both cases, the end result bore familiarity of form, but was lightyears ahead in terms of process and results.
The iPhone 5 is an almost entirely new, entirely redesigned phone. Watch this video, particularly the part at the end about how the iPhone 5 is produced.
That Ive and Apple could do this and still make it look so similar is a testament to their talent and the integrity of their vision.
Jony Ive and Apple have made a better phone. It's profoundly thinner, lighter, and stronger, with a faster radio, better battery life and camera optics, and more screen than ever before.
They've made a better iPhone.
They had to. It was inevitable.
Rene Ritchie is one of the most respected Apple analysts in the business, reaching a combined audience of over 40 million readers a month. His YouTube channel, Vector, has over 90 thousand subscribers and 14 million views and his podcasts, including Debug, have been downloaded over 20 million times. He also regularly co-hosts MacBreak Weekly for the TWiT network and co-hosted CES Live! and Talk Mobile. Based in Montreal, Rene is a former director of product marketing, web developer, and graphic designer. He's authored several books and appeared on numerous television and radio segments to discuss Apple and the technology industry. When not working, he likes to cook, grapple, and spend time with his friends and family.
Why do so many people hate the iPhone's night mode? Impressive engineering or an unnecessary gimmick?
This iPhone trick will make doing laundry easier— how to use Visual Look Up to get on top of your clothes pile
This man's wife found his 'deleted' iPhone messages on the family iMac, now he's suing Apple over his divorce


text: Mini Cooper Differences is a free online game from the genre of kids and car games. You need to keep locate differences between the two pictures in the limited amount of time given to play each time! To play, use your mouse as control. Make sure that you don't make a mistake more than five times because that will make you fail. 2 Minutes is the overall time in which you'll play through the ten pictures in this game! You can turn off the time limitation if you want to play the easier way. Good luck!


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COLUMBIA, Mo.–In general, it's a good idea for farmers to look at energy use on their farm every five years and consider opportunities to reduce energy consumption, says Don Day, energy extension associate for University of Missouri Extension.
However, the need for an energy audit may vary from farm to farm, Day said. For example, if a farmer already had an energy audit conducted on the farm, even if it was five or more years ago, it will continue to provide accurate information regarding potential energy savings until the farmer makes changes that affect energy usage.
"A new audit may also be in order if energy prices change or there is an additional energy alternative that a farmer is considering using that was not addressed initially," he said.
Changes in energy prices can alter payback periods, he added. "We have seen changes in the relative prices of energy sources over the past few years that will change what fuel a farmer might use." However, he notes, it generally doesn't pay to change the type of fuel you are using unless a piece of equipment such as a furnace or an engine needs to be replaced.
Day offers some additional recommendations to help farmers decide when they need an energy audit on their farm:
- Enterprises added to the farming operation after an original audit was completed need to be audited because they change total energy consumption.
- If a new farm location has been added to the farming operation, farmers should conduct an audit on the new location.
- When replacing equipment, consider energy use of the replaced components.
- New industry developments might necessitate a new energy audit or assessment. A good example is lighting developments (LED and CFL options) over the past few years.
- If farmers want to apply for a grant or loan for energy updates, they may need an updated energy audit or assessment.
For more information on energy audits, contact Don Day, energy extension associate with University of Missouri Extension, at 573-882-6385, or contact your local MU Extension center.
Read more http://extension.missouri.edu/news/DisplayStory.aspx?N=1655


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At a dramatic press conference on Monday, Israeli Defense Minister Ehud Barak announced his surprising resignation from politics after nearly 50 years in service of the country.
"I have decided to resign from politics and I will not be running in the [upcoming] elections," Barak told reporters at his office in the Defense Ministry headquarters in Tel Aviv. "I enlisted to the IDF in 1959 and I served the people of Israel for 47 years as well as I could."
The former prime minister reassured reporters that he would remain in his post until the establishment of the next government, following the Jan. 22 elections, and then "will free up time to focus on my family."
"I have exhausted my contribution to politics, which I was never entirely passionate about, and I feel that I must make way for others to man senior political positions. Turnover in positions of power is a good thing," Barak said, explaining the decision that took most Israelis by surprise.
While he took the time to dispel speculations suggesting that he would join up with other parties, insisting that he would not run in the election, Barak left the door open for a comeback by not saying explicitly that he would not return to politics. He said he was "at peace" with his decision, but that it did not come "without its misgivings."
"Thus I complete seven and a half years in the Defense Ministry, spanning three governments, one of them under my own leadership," he said.
Barak said he "led a systematic rehabilitation, bolstering the long arm and dealing with the Iranian threat, pushing Iron Dome and the other anti-missile interceptors and ensuring a deep diplomatic and military cooperation with the Americans."
"I want to thank from the bottom of my heart the IDF commanders, both in compulsory service and career soldiers, the people of the Defense Ministry and the members of the intelligence community, who allowed me to fulfill my duties as defense minister successfully. I am proud to have led such wonderful people. I want to thank the prime minister and my colleagues in the government, as well as my devoted friends in the Independence Party leadership, who gave me a lot of strength for many years and for long hours," Barak added.
The political echelon did not waste a second before issuing responses to Barak's dramatic announcement, with Labor Chairwoman Shelly Yachimovich expressing her sorrow over Barak's resignation even before the press conference ended.
"Barak is the world's most decorated soldier, and one of the most highly regarded defense figures in the international community. He contributed to the IDF and to the security of the country more than the public will ever know," Yachimovich said.
Prime Minister Benjamin Netanyahu also voiced his appreciation for the outgoing minister, saying, "I thank him for his cooperation and I very much appreciate his longtime contribution to the security of the state."
But not all the responses were sympathetic. MK Danny Danon (Likud) issued a statement shortly after the announcement, declaring, "Thank God we are rid of this nuisance."
"After Barak realized that he could not secure a seat on the Likud list he understood his irrelevance in the political arena and decided to initiate his resignation, instead of the people forcing it upon him," Danon said in a statement.
Likud minister Yuli Edelstein echoed his colleague's sentiments, saying, "Today is a day of independence for Likud."
"Barak will go down in the annals of Israel's governments as the worst defense minister in the history of the Jewish settlement enterprise. His conduct was rife with egotistical and political considerations, all at the expense of the Jewish settlers," said Edelstein. "I wouldn't be surprised if, at the first opportunity, he will find a reason to return to politics and to his evil ways."
The Strong Israel faction, headed by rightists Aryeh Eldad and Michael Ben-Ari, also issued a celebratory response, adding that "now Netanyahu and [Foreign Minister Avigdor] Lieberman will be able to approve all the construction plans for Judea and Samaria that had gotten bogged down on Barak's desk. Or, alternately, it may emerge that Barak was only a fig leaf and that it was the prime minister himself who was responsible for the mistreatment of the settlers."
On the other side of the political spectrum, Israel's Left was no less critical of the resigning minister. "Barak played a dual role in the political system," said Meretz Chairwoman Zahava Gal-On. "I commended him as the one who normally blocked extreme policies, but sometimes he was the one who spearheaded extreme moves and pushed them forward."
"There is something symbolic about the fact that Barak, the man who invented the 'no partner' spin, the man who disappointed and failed to sign a peace agreement with the Palestinians, who didn't end the occupation the way we expected him to, is resigning precisely in the same week his 'partner' [Palestinian Authority President] Mahmoud Abbas extends a hand to peace with Israel and seeks recognition of the PA as a state. Now Barak is gone, just when he gets a chance to rectify the historic damage he caused," Gal-On said.
Hadash Chairman Dov Khenin said, "Ehud Barak was the pillar that made possible the existence of the most extreme rightist government in Israel's history. He will never be able to absolve himself of this historic responsibility. Barak's political maneuvering cannot mask his culpability for the four difficult years of frozen diplomacy, the damage he caused to the possibility of peace with the Palestinians and the general economic and social deterioration."
The news even elicited a response from Gaza. Hamas spokesman Fawzi Barhoum said that Barak's resignation was yet another victory for the Gaza terror organizations, Israel Radio reported. He explained that the resignation was proof that Israel's recent Gaza Strip offensive, which Barak led, had been a failure.


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NASHVILLE, Tenn. (AP) — After a spring-like tease, the emerging weather pattern over Tennessee is a reminder it's still winter.
Some significant precipitation and much colder temperatures are moving into the state and there could be a bit of snow into the weekend in Middle and East Tennessee.
John Cohen, with the National Weather Service in Nashville, said a potent upper-level storm system that was dumping snow on the Texas and Oklahoma panhandles Monday would influence Tennessee's weather.
However, Cohen said, the inches of snow coming down in the plains won't happen in the Volunteer State.
"Given the track of that low, it's going to move toward to the Missouri boot heel and into the Ohio Valley," Cohen said. "That leaves Tennessee on the warmer side."
The result, said Cohen, will be widespread rainfall that could exceed an inch in places with possible thunderstorms.
Rain on Monday afternoon in the Memphis region will overspread the state in the next couple of days as temperatures tumble from near 60 at Memphis to freezing or below by midweek across Tennessee.
As the rain moves through Middle Tennessee overnight Monday into Tuesday, forecasters said sustained winds around 15 mph were expected, but gusts up to 40 mph would be likely.
From the Tennessee River eastward, a mixture of rain and snow is possible by Wednesday night.
The energy waves continue as the temperature drops and there could be snow on the ground by the weekend.
Cold weather is coming


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Jack Henry Launches Expedited EMV Implementation
Payment Processing Solutions (PPS), a division of Jack Henry & Associates (JHA), has announced an expedited EMV implementation process of U.S. chip card issuance.
According to Jack Henry, it can conduct EMV implementation for U.S. financial institutions that issue Visa-branded cards, and the process does not require direct project involvement by card brands for the install.
"Everyone's eyes are on EMV right now and it is only a matter of when for the U.S. financial institutions that have yet to adapt the cards,' said John Postle, general manager of PPS, in a statement.
PPS said it had to complete a U.S. chip issuance project with Visa to qualify. PPS allows banks and credit unions to consolidate at a point of contact for settlements, adjustments, and reconciliations.
EMV, the global technology standard for credit and debit card payments named after its original developers (Europay, MasterCard and Visa), features cards with embedded microprocessor chips that store and protect encrypted account user data, in contrast to the magnetic strip cards now used mostly in the U.S.
[Related Content: EMV Implementation: Who Is Ready?]
Zarna Patel is a staff writer for InformationWeek's Financial Services brands, which include Bank Systems & Technology, Insurance & Technology and Wall Street & Technology. She received her B.A. in English and journalism from Rutgers University College of Arts and Sciences in ... View Full Bio


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Gadgets! More gadgets and kitchenware. More plates, bowls, silverware and cups. Ice-cream maker, blender, electric whisk, puree machine and the rice cooker.
No - I am not taking inventory!
I am a kitchenware and gadget hog. I do not collect unnecessarily of course, only things I need. Tom might actually argue with that because a man cannot begin to understand that we need more than one knife and tart forms in small, medium and large are totally required. Even my prop box, the one with individual dishes and bowls for my photography, is totally necessary. I admit lately it has become a bit more than just a box - it has extended to a larger drawer space in the living room AND the box.
I have however, made a promise to myself. After my pasta machine arrives, I will stop hogging. But then I saw the Browniebabe Apron and knew it had to adorn my kitchen. I wanted to be a browniebabe. Unfortunately I missed the first one, but decided the second round of this fantastic event, created by the lovely Myriam, was one event I just needed to take part in.
I went in search of the ultimate brownie, what I found was a "whitie" from the brilliant Dorie Greenspan and her incredible Baking: From My Home To yours. Ever since I got my hands on the book I have been making a few incredibly delicious things. I will forever be indebted to Sara!
The past few months however, although I have referred to the book for several things (the book is filled with a wealth of knowledge) I have not made much from it. Shame on me! As my copy of the book is covered with post-its in several colors, highlighting all the recipes I still would like to make. So, without much ado I decided to turn to Dorie to help me find the perfect brownie recipe. And she did not let me down. This wonderful white chocolate brownie speckled with fruity raspberries is decadent and rich. Dotted with a raspberry coulis it becomes an elegant party dessert.
Dorie herself describes this just wonderfully:
The cake layer is slender, delightfully dense and both sweet and tart; the meringue is soft and golden. You can tell them brownies, but serve them with a swirl of raspberry coulis and they'll be worthy of a black-tie gala.I do not often make desserts or cakes with white chocolate and this prompted me to go in search of this ingredient.
White Chocolate
White chocolate officially is not chocolate at all. To be called "real" chocolate it needs to contain chocolate liquor, which is what gives it the bitter intense chocolate flavor and color to dark and milk chocolates. Good quality white chocolate contains cocoa butter, milk solids, sugar, lecithin and flavorings, usually including vanilla. Cocoa butter is the fat from cocoa beans, extracted from the cocoa beans during the process of making chocolate and cocoa powder. Cocoa butter has very little 'chocolate' flavor. When buying white chocolate check the label to see if it contains cocoa butter as some inferior brands contain vegetable fat.
White chocolate is is ivory in color and rich and creamy in texture. It is a difficult product to work with when baking as it scorches easily, causing the cocoa butter to split and create an oily compound that cannot be recovered and must be discarded. Therefore, it is recommended to work with high quality brands of white chocolates. I use the brand Lindt, which is also available in the US.
Well with that knowledge and Dorie's help I think I have a pretty good looking and darned great tasting little brownie.
White Chocolate Brownies
Adapted from Dorie Greenspan's Baking: From My Home To yours
70g (2/3 cup) all-purpose flour
85g (1/2 cup) finely ground almonds
115g (8 tablespoons) unsalted butter
1/2 teaspoon salt
113g (4 ounces) premium-quality white chocolate - coarsely chopped
190g ( 1 cup) sugar
2 teaspoons grated orange zest
4 large eggs
1 vanilla bean - insides scraped
200g (1 cup) fresh raspberries
3 large egg whites - room temperature
Pinch of salt
95g (1/2 cup) sugar
Center a rack in the oven and preheat it to approx 170 degrees C. Butter a rectangular pan, about 9x13 inch and line the bottom with parchment paper. Butter the paper and dust the bottom and sides of the pan with flour, tapping out any excess. Place the pan on a baking sheet.
In a bowl, mix together the flour, ground almonds and salt. Allow some water to gently simmer in a saucepan, set a heatproof bowl over this creating a water-bath. Place the butter in the bowl and add the chopped chocolate, stirring frequently until the chocolate had just melted. Do not allow the mixture to get to hot, otherwise the chocolate and butter will separate. As soon as the chocolate has melted remove from heat.
In another large bowl rub the sugar and orange zest together with your fingers until the sugar is moist and aromatic. Add the eggs and with an electric whisk or hand mixer beat on medium-high speed for approx. 3 minutes until pale and foamy. Add the vanilla and then reduce the mixer speed to low and add the chocolate mixture. Mix in the dry ingredients, stirring only until they disappear into the batter. Scrape the batter into the prepared baking pan and sprinkle evenly with raspberries. Set aside while you get the meringue ready.
In a clean bowl, using a clean whisk attachment or beaters, beat the egg whites with a pinch of salt on medium speed until foamy and turn opaque. Increase the speed to medium-high and slowly add the sugar in a steady stream. Whip the whites until they form firm, glossy peaks.
Gently spread the meringue over the brownie batter.
Bake for 30 - 35 minutes, until the meringue is browned and crackly and the brownies pull away from the sides of the pan. Allow to cool on a rack.
Gently turn the brownies out on to the rack, making sure not to squish the meringue. Peel away the parchment paper lining and carefully invert the brownies onto a cutting board. Cut into approx. 32 bars.
Raspberry Coulis
250g (2 cups) fresh raspberries
35g (3 tablespoons) sugar
Put the berries and sugar in a blender or food processor and blend until pureed. Taste and mix more sugar if required. Press the coulis through a strainer to remove the seeds.
Swirl some of the fresh coulis over a brownie and enjoy!
A wonderfully sweet dessert cake. There is nothing normal about this brownie - it's soft, moist and cake like texture goes perfectly with the slight tanginess from the raspberries and the coulis adds perfect elegance to it. I think when I said we were making brownies to Soeren and produced this there was a seconds disappointment, after one bite there was nothing but pure satisfaction on his face. Even Tom had this "Get outta here!" look on his face when I told him it was a brownie.
EBBP News
For those of you in Europe taking part in this round of EBBP are probably keen on knowing what I sent, to who and what I got from whom. As always it was a lot of fun packing away a little something to my parcel partner who had no idea from which European destination the package would be arriving. And it was even more exciting waiting for the mailman to bring a package to my doorstep. Johanna of The Passionate Cook set a theme this time - "Childhood Sweets"
Curious to see what was in my parcel and where it went? Click here for more.
My parcel made it's way all the way from the UK. It came from a wonderful blogger I have had the pleasure of recently getting to know. She is simply lovely and a few days ago I found out that she celebrates her birthday just a day before mine!
Abby from Eating The Right Stuff packed together a lovely parcel for me. She was so thoughtful to even pack a small birthday cake from Konditor & Cook for me - god I was touched. So, as I devoured the cake I inspected the rest.
Abby grew up in Malawi and says:
I grew up in Malawi and sweets and chocolates were very scarce.So, she racked her brains and sent me some African bubble gum and lollipops. She also packed some Rowntrees fruit pastels and gums:
When we went to the cinema I remember my mum buying boxes of Rowntrees fruit pastels and fruit gums. The pastels were for my brother and I and the gums for my mum.There was also a bar of Green & Black's cherry chocolate, some natural chips, seed biscuits and lovely Damson fruit cheese. I am not sure about the Gentlemen's Relish though
a bit of an oddity ... it's an anchovy paste which my father used to smear very thinly on buttered toast.Abby for you I will give the paste a try!
I thank you for this wonderful package and your thoughts. I enjoyed reading about the sweets in your life and simply look forward to getting to know you more.
Technorati Tags: brownie, browniebabe, white chocolate, raspberry, cake, dessert, bake, baking, food, recipe, food blog, photography, nikon d70s
All photographs and written content on What's For Lunch, Honey? © 2006-2007 Meeta Albrecht unless otherwise indicated. | All rights reserved | Please Ask First


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Americans spent over $53 billion on pets last year
Pet group says Americans spent over $53 billion on their pets last year, up 5 pct from 2011
LOS ANGELES (AP) -- The economy may have remained sluggish last year but Americans refused to scrimp on their pets, with animal lovers spending upwards of $53 billion on food, veterinary care, kennels and other services in 2012.
That's up 5 percent from 2011, when spending first broke the $50 billion barrier, says the American Pet Products Association, a trade group based in Greenwich, Conn. And APPA President and CEO Bob Vetere predicts another 4 percent gain this year.
At about $34.3 billion, food and vet care represented about two-thirds of total spending, with money spent on supplies and over-the-counter medications rising by more than 7 percent. Spending on the growing market of alternative vet care, such as acupuncture, totaled about $12.5 billion.
Vetere says spending on services like grooming, boarding, hotels and pet-sitting grew nearly 10 percent during 2012 to almost $4.4 billion.


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Leaves are falling in the summertime. School starts in early August in many places. Politicos are already talking about the presidential election — of 2016.
Everything is happening earlier.
According to various reports, the allergy season, the NFL season and the winter holiday shopping season seem to be occurring earlier. Fact is, all seasons — winter, spring, summer and fall – are showing up sooner.
"The seasons are coming earlier on land than they used to," says Alexander Stine of Harvard University's Department of Earth and Planetary Sciences, "because of changes in patterns of global winds over the last half century."
As the winds sweep across the planet, he explains, "they carry differing amounts of heat with them — depending on where they come from — and can thereby modulate when things warm up or cool down. In particular, the changes in the winds have been biggest at the end of the winter and have sped up the arrival of spring."
A 2009 analysis of global temperatures between the years 1850 and 2007, authored by Stine and others, reveals that the seasons are showing up about two days earlier than they were 50 years ago.
Physiologically, financially, culinarily — life is happening earlier. A recent New York Times story reports that the breasts of young American girls are developing earlier. Because of hypertechnology and global markets, we get financial information earlier. McDonald's just announced it is serving breakfast beginning at midnight instead of 5 a.m.
Earlier than ever, we get: news of the world, new books to read and new music to listen to.
What effect will all of this earliness ultimately have on our culture? In many ways, it's too early to tell.
Earliness Can Really Bug You
We do know this: There can be repercussions when the seasons arrive earlier.
The cherry tree blossoms in Washington, D.C., for instance, are trending earlier and earlier. The Washington Post reports that in 2012, the iconic trees bloomed five days earlier than they did in 1921, the first year that records were kept.
And summer pests appeared earlier than usual this year. Missy Henriksen of the National Pest Management Association, explains that according to the NOAA National Climatic Data Center, the first half of 2012 was the warmest on record for the U.S. mainland since record keeping began in 1895.
"Many parts of the country enjoyed a winter season that kept children in flip-flops instead of snow boots," Henriksen explains. "One of the consequences of the unseasonable winter temperatures is that it caused an early emergence of numerous species of bugs."
Insects are cold blooded, she says, so "they look to cues from Mother Nature to direct their biological functions. While calendars may have said February, mercury readings said June and accordingly, many insects arose from their over-wintering state weeks — and in some cases months — earlier because of the warm weather."
She says termites, mosquitoes, ants, ticks and fleas were all out in force ahead of schedule.
Henriksen didn't mention worms — perhaps they were gotten by early birds.
Fast Track To ... Failure?
Early birds, however, will not be encouraged this time around to line up at midnight for the release of the LeBron X or other new Nike sneakers. The Wall Street Journal and others report that Nike has put an end to that popular practice because of security concerns.
But prospective college students, like the ninth-grader mentioned in this New York Times piece from earlier this year, are looking at possibilities at a younger age. And in turn, SB Nationreports, colleges are looking at young people earlier. The Times also reports a notable rise among some universities in early admission applications.
"Better three hours too soon than a minute too late," William Shakespeare wrote in The Merry Wives of Windsor. Leave it to Shakespeare to point out a virtue of earliness
Early Americans bought into this reverence for earliness. "Early to bed and early to rise," Ben Franklin famously claimed, "makes a man healthy, wealthy and wise."
Later Americans also embraced earliness. Tycoon J. Paul Getty is reported to have put his formula for success in six words: "Rise early, work hard, strike oil."
And so we much-later Americans still feel in our national DNA a rush to earliness. We grow up earlier. Eat breakfast earlier. Get into college earlier. Go to work earlier. The quest for ever-earlier earliness is a lifelong pursuit.
There can be drawbacks. Sometimes it's just too soon for a bird to fly. Or it's premature to eat a persimmon. Or it's too early for a Major League pitcher to pitch a full season. Never serve a wine before its time and all that.
Eagerness for earliness can lead to failure — in a hurry.
Leave it to Shakespeare again to point out a fallacy of earliness. In some instances, it can be just another shade of lateness. "I am glad I was up so late, for that's the reason I was up so early." Shakespeare wrote in Cymbeline.
That, of course, was one of his late plays.
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