Benchmarking of Red-colored Bridges

While being stuck in traffic at the Golden Gate bridge during my last San Francisco trip, an idea occurred to me. How about I do some research work to benchmark all suspension bridges in the world?

A quick check at Wikipedia gave me over one hundred candidates, leading me to restrict my ambitious plan [...]

Posted on 20 August 2014 | 1:17 pm

An Algorithmic Comparison of BLASR/BWA-MEM, DALIGN and MHAP

The problem of assembling a large number of noisy long reads is expected to show up, no matter whether one uses Pacbio or nanopore long read technology. The good news is that it is possible to do the assembly and the quality is a lot better than what can be achieved with short reads or [...]

Posted on 20 August 2014 | 12:39 pm

Biology Student Faces 8 Years in Jail for Posting Scientist’s Thesis on Scribd

Remember TPP? Here is a good example of what ‘free trade’ will look like after all countries adopt the rules written by multinational corporations.

A Colombian biology student is facing up to 8 years in jail and a fine for sharing a thesis by another scientist on a social network.

Diego Gómez Hoyos posted the [...]

Posted on 19 August 2014 | 8:44 am



Influence of RNA Extraction Methods and Library Selection Schemes on RNA-seq Data

We came across this BMC Genomics paper in twitter, but did not get time to read yet. Hopefully, the readers will find it useful.

Background Gene expression analysis by RNA sequencing is now widely used in a number of applications surveying the whole transcriptomes of cells and tissues. The recent introduction of ribosomal RNA [...]

Posted on 12 August 2014 | 9:49 am

Benchmark Analysis of RNA-Seq is an Excellent Confirmation of ‘Short Read’ Noise

In the past, we talked about ‘short read noise’, which is the noise introduced by clean short reads due to being short. Readers may take at these two of our earlier commentaries for details.

End of Short-Read Era? – (Part I)

End of Short-Read Era? – (Part II)

An excellent biorxiv paper analyzing RNA-seq assemblies [...]

Posted on 16 July 2014 | 3:14 am

‘Transcriptome Assembly is Hard’, but Not Any More with Richard Smith’s Transrate

Richard Smith-Una, whose work was covered in our blog, releases a new quality assessment program (transrate) that we surely like to check out.

Transcriptome assembly is hard. The algorithms are complex, the data are messy, and it’s often not clear how to determine whether an assembly is suitable for answering a biological question.

Transrate [...]

Posted on 8 July 2014 | 7:53 am



Shadow Enhancers Enable Hunchback Bifunctionality in the Drosophila Embryo

The following new paper is posted in arxiv. When bifunctional transcription factors activate and repress target genes within the same cell, these opposing activities must be encoded in regulatory DNA. Here, we use cellular resolution gene expression data and computational...

Posted on 13 August 2014 | 7:06 am

Evolution of my Little Pet Dinosaur

Sustained miniaturization and anatomical innovation in the dinosaurian ancestors of birds Recent discoveries have highlighted the dramatic evolutionary transformation of massive, ground-dwelling theropod dinosaurs into light, volant birds. Here, we apply Bayesian approaches (originally developed for inferring geographic spread and...

Posted on 2 August 2014 | 9:43 am

Adam Smith and Theory of Evolution

What role did Adam Smith play in helping Darwin develop his theory of evolution? Quite a bit actually. If you think carefully, you will see many similarities between Adam Smith’s ‘The Wealth of Nations’ and Darwin’s theory of natural selection....

Posted on 29 July 2014 | 3:22 pm



BioXSD: the common data-exchange format for everyday bioinformatics web services

A paper on common standards came out in 2010 in Bioinformatics. It is being discussed in #socbin14 conference. Isn’t JSON more appropriate? Motivation: The world-wide community of life scientists has access to a large number of public bioinformatics databases and

Posted on 12 June 2014 | 3:43 am

d3.js – Tutorials, Books, Examples

d3.js is a SVG-based framework. 1. mbostock/d3 github gallery This is the best source for hands on learning and comes from the author of d3.js. There are many examples to choose from and study their codes. We have been going

Posted on 6 May 2014 | 11:28 am

We Plan to Be Early Adopters of Meteorchart

Earlier we talked about HTML5 and SVG, as well as kinetic.js, raphael and d3.js. Eric Rowell, the author of kinetic.js, developed a new program called Meteorchart, which seems interesting. We plan to use it for our bioinformatics applications. The program

Posted on 3 May 2014 | 7:21 am



Non-random DNA fragmentation in next-generation sequencing

link

Next Generation Sequencing (NGS) technology is based on cutting DNA into small fragments, and their massive parallel sequencing. The multiple overlapping segments termed “reads” are assembled into a contiguous sequence. To reduce sequencing errors, every genome region should be sequenced several dozen times. This sequencing approach is based on the assumption that genomic DNA [...]

Posted on 10 June 2014 | 6:08 am

PacBio P4-C2, P5-C3, etc. – What Do They Mean?

We had been pondering about those cryptic terms and found by asking some people around that the P stands for polymerase and C stands for chemistry. Therefore, P4-C2 means polymerase of fourth generation and chemistry of second generation.

Polymerase

That got us curious about what the actual DNA polymerase sequences are for 2nd, 3rd or [...]

Posted on 4 April 2014 | 4:58 am

Three Amazing Applications of CRISPR/cas9

Changing genome in plants used to be incredibly difficult, but not any more. Here is an excellent review -

Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system

Targeted genome engineering (also known as genome editing) has emerged as an alternative to classical plant breeding and transgenic (GMO) [...]

Posted on 31 March 2014 | 9:58 pm



Lorenz Attractor Spreading into Chaos

h/t: @infoecho

Posted on 28 July 2014 | 11:47 pm

Branches of Mathematics and Fermat’s Last Theorem

In the next few months, we like to go over Andrew Wiles’ proof of Fermat’s last theorem. For the time being, let us consider the evolution of various branches of mathematics and a very short intro of the proof. History...

Posted on 7 July 2014 | 1:23 pm

For Your Summer Reading – A Few Well-written Math Books

1. Visual Complex Analysis – Tristan Needham 2. Learning Modern Algebra – Couco and Rotman 3. Naive Lie Theory – John Stillwell 4. Nonlinear Dynamics and Chaos – Steven Strogatz 5. Concrete Mathematics: A Foundation for Computer Science – Ronald...

Posted on 7 July 2014 | 1:13 pm



Early Evolution of Fish – A Primitive Fish from the Cambrian of North America

New Nature paper - Knowledge of the early evolution of fish largely depends on soft-bodied material from the Lower (Series 2) Cambrian period of South China1, 2. Owing to the rarity of some of these forms and a general lack...

Posted on 12 June 2014 | 3:48 am

The Fishiest Story Ever – (ii)

This is a follow up of previous commentary – The Fishiest Story Ever – (i). All orders of fish are shown below based on the following phylogeny (courtesy: Professor James Albert). Please note that we (humans, tetrapods) are also a...

Posted on 7 May 2014 | 7:48 pm

Rare Megamouth Shark Caught in Japan

Source Megamouth shark was first seen in 1976 and is so rare that - According to WPTV, it was only the 58th megamouth to have been captured or sighted by man. The Florida Museum of Natural History states that the...

Posted on 7 May 2014 | 7:38 pm



With 72x Genome Duplication, Why Isn’t Rapeseed Smarter than Us?

Seems like we need another ENCODE project here. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling,...

Posted on 21 August 2014 | 5:21 pm

Genomic-scale Exchange of mRNA Between a Parasitic Plant and its Hosts

A new paper published in Science shines light on horizontal gene (mRNA) transfer between parasitic plant strangleweed and its host (h/t: Keith Robison). Movement of RNAs between cells of a single plant is well documented, but cross-species RNA transfer is...

Posted on 16 August 2014 | 6:34 pm

Immune System in Plants – A Good Review from 2011

We earlier posted on the possibility of LRR-type immune system of Ectocarpus. Readers may find the following review useful in that context. Arabidopsis and the Plant Immune System Notes. 1. The first challenge was to dispel the notion that Arabidopsis...

Posted on 8 July 2014 | 10:55 am



Subprime Loans Are Just the Start of the Massive Student Debt Scam

Wall Street Examiner covers this analysis - This is amazing. If you thought there was only one component to the gargantuan student debt scam, think again. Because here’s the thing: If you’re about to become a college student, if you’re already a college student, or if you’re simply in debt and need more credit and plan on becoming a student again, you’re in luck. Financial services giants Discover Financial Services Inc.(NYSE: DFS), Capital One Financial Corp. (NYSE: COF), Bank of America Corp. (NYSE: BAC), Citigroup Inc. (NYSE: C), and U.S. Bancorp (NYSE: USB), to name a few players in the student credit game, are bending over backward for you. The folks at Discover want you to “Get the card for college and beyond.” They’ve named and registered it as “Discover It Chrome for Students” because, after all, they’re “Looking out for you.” But they aren’t the only do-gooders looking out for you. You can also apply for the Capital One Journey Student Rewards Credit Card, the Bank of Americard for Students, the U.S. Bank College Visa Card, or the Citi Dividend Platinum Select Visa Card for College Students. Heck, why not apply for all of them? But wait. Before switching [...]

Posted on 11 August 2014 | 5:15 pm

Californian Parents Realize They Are on Hook for $100K Student Loan after Daughter Dies Unexpectedly

Only in California - A California couple is speaking out after they say their finances have been devastated over their daughter’s student loan debt, which they are being forced to repay after the woman died unexpectedly four years ago. Steve and Darnelle Mason’s 27-year-old daughter Lisa died suddenly from a liver disease, leaving behind three children. Darnelle Mason, who is now raising her grandchildren along with her husband, told Fox Business the “excruciating” pain of losing her daughter has only been compounded by the crushing debt. “She was doing what she really loved to do,” Mason said. “So it is really just a crushing burden.” Lisa Mason had taken out close to $100,000 in student loans in order to pay for nursing school, and was making payments on the debt when she died. Steve Mason said he and his wife, who had co-signed the loans, were contacted immediately after his daughter’s death and were told they must start making payments. Market-ticker blog responds: Now, You Understand…. I find it utterly disgusting that people have to be personally cornholed before they will stand up and take a position to do the right thing. Lisa Mason had taken out close to $100,000 [...]

Posted on 11 August 2014 | 5:11 pm

Don’t Send Your Kid to the Ivy League – Former Yale Professor

“The nation’s top colleges are turning our kids into zombies” says William Deresiewicz. His wiki profile describes him as - Career Academia In 1998, Deresiewicz joined the faculty of Yale University. He taught courses in modern British fiction, Great Books, Indian fiction, and writing, among other areas.[10] He left academia in 2008 to become a full-time writer. We would advise dumping the rest of the colleges as well, but let us at least read the rest of the story of what he saw before leaving Yale. The sign of the system’s alleged fairness is the set of policies that travel under the banner of “diversity.” And that diversity does indeed represent nothing less than a social revolution. Princeton, which didn’t even admit its first woman graduatestudent until 1961—a year in which a grand total of one (no doubt very lonely) African American matriculated at its college—is now half female and only about half white. But diversity of sex and race has become a cover for increasing economic resegregation. Elite colleges are still living off the moral capital they earned in the 1960s, when they took the genuinely courageous step of dismantling the mechanisms of the WASP aristocracy. The truth is [...]

Posted on 28 July 2014 | 3:02 pm



Has Ebola Reached India – World’s Second Most Populous Country?

Times of India reports - 3 Ebola suspects at Ram Manohar Lohia Hospital NEW DELHI: Three persons from Ebola-affected Nigeria, who arrived here Saturday morning, have been admitted to the Ram Manohar Lohia Hospital for screening and treatment if required. The three Nigerians, aged 79, 37 and 4 years had fever and their tests were being done at the National Centre for Disease Control (NCDC), Delhi, an official release said here. In addition to this, a 32-year-old Indian from Durg in Chhattisgarh who returned from Nigeria has been admitted to a hospital in Bhilai. His samples are also being tested at NCDC, the release said.

Posted on 17 August 2014 | 9:22 am

Conspiracy Theory Monday – US “Likely Hiding Truth” on MH17

Ron Paul, a certified conspiracy theorist, published a short message on the Malaysian Airlines plane shot over Ukraine. August 7, 2014 – The U.S. government5016239182_e58d8c9abf_z has grown strangely quiet on the accusation that it was Russia or her allies that brought down the Malaysian airliner with a buck anti-aircraft missile. The little that we have heard from U.S. intelligence is that it has no evidence that Russia was involved. Yet the war propaganda was successful in convincing the American public that it was all Russia’s fault. It’s hard to believe that the U.S., with all of its spy satellites available for monitoring everything in Ukraine that precise proof of who did what and when is not available. When evidence contradicts our government’s accusations, the evidence is never revealed to the public—for national security reasons, of course. Some independent sources claim that the crash site revealed evidence that bullet holes may have come from a fighter jet. If true, it would implicate western Ukraine. Questions do remain regarding the serious international incident. Too bad we can’t count on our government to just tell us the truth and show us the evidence. I’m convinced that it knows a lot more than it’s [...]

Posted on 11 August 2014 | 8:21 pm

Future of US Economy Shown in One Long-term Chart

Deflation is knocking on our door – says Jas Jain in “Growth and Inflation In America: Why Deflation Is Knocking at the Door and Going to Burst Through“. The above chart is self-explanatory, but if not, please take a look at his article at safehaven. Jas is famous for coining the words ‘peak debt’ in 2005, when everyone else was busy worrying about peak oil and other spurious peaks.

Posted on 11 August 2014 | 12:50 pm