HarvardX Biomedical Data Science Open Online Training

Genome-wide methylation data mirror ancestry information

novel method developed within the MAQC-III project utilizing the expression distributions, corrected for noise and batch effects, and assisted by random resampling, to compute DEG scores related to the Wilcoxon U test (Magic, see Additional file 1: Supplementary Note 2)

MOSAiCS implements a model-based approach where the background distribution for unbound regions take into account systematic biases such as mappability and GC content and the peak regions are described with a two component Negative Binomial mixture model

EXCAVATOR: detecting copy number variants from whole-exome sequencing data

Robust enumeration of cell subsets from tissue expression profiles

AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number

CIBERSORT, a computational approach for inferring leukocyte representation in bulk tumor transcriptomes

SomaticSniper

afocusontheanticipatoryandthefuturesuchthatmoreemphasisisgiventopredicting,intervening,andmanagingconsequencesratherthanunderstandingcauses;andthemoreeasyandsuccessfuladoptionandadaptionofdatatodifferentfieldswithlittlerisk

Salmon provides fast and bias-aware quantification of transcript expression

applying networkand content analyses

KaryoStudio

argyle: An R Package for Analysis of Illumina Genotyping Arrays

Analysis of LMS Categories of Function

ocial networks is relational data

The projection score - an evaluation criterion for variable subset selection in PCA visualization

contort

While technology has loomed large in these accounts, several scholars argue that this shift toward participation extends important possibilities for posi-tively influencing daily life (Jenkins, 1992, 2006; Shirky, 2010). Others question the ability for a universal “participation” within new media cultures, suggesting people require adequate social and psychological resources, including time, for engagement (Irani, 2015; Turner, 2009).

Organizations such as Code for America (CfA) rallied support by positioning civic hacking as a mode of direct partici-pation in improving structures of governance. However, critics objected to the involve-ment of corporations in civic hacking as well as their dubious political alignment and non-grassroots origins. Critical historian Evgeny Morozov (2013a) suggested that “civic hacker” is an apolitical category imposed by ideologies of “scientism” emanating from Silicon Valley. Tom Slee (2012) similarly described the open data movement as co-opted and neoliberalist.

RCP: a novel probe design bias correction method for Illumina Methylation BeadChip

The ISMARA client

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs

Introduction to R for Data Science

Learn Data Science Online

($20*3)-($20*3*.1) = $54

National Center for Policy Analysis

National Center for Policy Analysis

The reason this was possible in my view was that the Prophet understood that his power had no limits, since the source of it was the uniquely omnipotent divine source of all power: Allah.

National Center for Policy Analysis

En un lugar de la Mancha, de cuyo nombre no quiero acordarme,

I'm the developer of pyGeno. Here's a little script that does just that for the Gene TPST2, by using segment trees

The Google Analytics Setup I Use on Every Site I Build : 글쓴이가 수없이 웹사이트에 GA를 설정해 보면서 얻는 경험으로 GA 스크립트의 로딩 자체를 최적화하는 방법과 커스텀 디멘션을 사용해서 유용한 추적설정을 한 내용을 모두 설명하고 있다. 설정 방법과 어떻게 보고 참고할 수 있는지까지 잘 나와 있어서 웬만한 사이트는 이 글의 내용을 그대로 따라 해도 될 정도고 여기 나온 내용을 바탕으로 사이트에 필요한 추적을 추가하기에도 좋다. 이 사람은 GA를 엄청나게 연구했는지 비슷한 작업을 매번 하다가 결국 autotrack 플러그인을 개발했고(이 플러그인만 사용해도 엄청 편하다) 이 글에서 설명한 코드를 참고할 수 있도록 analytics.js boilerplate를 만들어서 공유하고 있다.(영어)

In his introduction to “What We Do Now,” co-editor Dennis Johnson writes of the widespread “despair,” “grief” and “disillusionment” that followed the election.

Again I say, this is harmful,\ since the invention of arguments is by nature prior 10 the judgment of their validity,

I started using Google Maps because of the ease of dragging the map. But Google Maps didn't require me to sign-up or join as a member.

evidence about obtaining higher productivity by using Agile methods

blast

One of the distinct pleasures in Pixar’s films is the pleasure of seeing the deepest of human struggles, timeless philosophical questions projected in and through remote forms of representation.

Pixar’s Toy Story (Dir. John Lasseter, 1995) and WALL-E (Dir. Andrew Stanton, 2008) are “innocent” animated film about ob-jects, their value as cinema lies in their ability to complexly address human—and sometimes wholly adult—fears about meaninglessness, apocalypse, and oblivion.

riveting mounds of metal dramatically revealed through the birds-eye shots that rival the buildings in height—are actually mile-high piles of trash.

In WALL-E, the humans have converted themselves into floating objects—mounds of flesh laden with too many conveniences to move for them-selves.

Toy Story 3 (2010) be-gins with Andy’s toys playing pretend. The setting is the Old West. Sheriff Woody fights the Potato Heads-cum-bandits to rescue a moving train full of orphan trolls. The Potato Heads escape the train in Barbie’s dream car. But the train is headed toward the precipice at the end of a dynamited trestle. Despite Woody’s efforts, the train plunges off the edge. We hear it thud below and see smoke rise from the chasm. Cow-girl Jessie’s jaw drops in utter disbelief and disappointment. For several long seconds as the energy of the action se-quence diffuses, we believe that Woody has failed. Then Buzz lifts the train out of the hole. But the threat is not, as we had imagined, contained but is instead reanimated and escalated. The toys are assailed by a mushroom cloud of “death by monkeys” and finally an unnamed threat behind a red button in Evil Dr. Porkchop’s dirigible.

Jessie perhaps best ar-ticulates the pleasure of being a toy, an object used for the innocent pleasure of others: “Even though you’re not mov-ing, you feel alive because that’s how they see you.” With this statement Jessie highlights with a disarming frankness the philosophy of being the animated toy. She reveals how remote, ocular con-trol paradoxically creates a kind of inti-macy and movement that is enviable—revealing self to self through shared, pretend movement.

Perhaps more persuasive even than these final lines, are the final shots of the film in which the sparkling out-fits of the sequined trio of Barbie dolls mix with the starry wall-paper of the room, suggesting the space-like infinity to which Woody refers.

Since Amy becomes a mirror to Sheldon, she must be intelligent, but her showings of this intelligence can be awkward.

According to Sherri Inness, “Lisa Simpson of The Simpsons is one of the most influential smart female characters on television, but she is not depicted entirely posi-tively, being too studious and serious when compared with her brother Bart”

For Bernadette, the roles of caretaker and mother offer little to no appeal.

Sheldon remains awkward and unclear in its trajectory. Amy desires a more traditional relationship than what Sheldon currently offers, but Sheldon remains avoidant or clueless about those conventions

and even families

the classic plot situa-tion of the boyfriend trying to find a way to make up his poor behavior to his girl

t the end of season 4, Berna-dette announces that she successfully defended her dissertation and earned her Ph.D., and she then announces being recruited by a pharmaceutical company and getting paid a “buttload” of money. This announcement becomes an oppor-tunity to deride Howard (yet again) for his lack of Ph.D. and his less-significant career.

She visits Leonard’s lab to learn more about his experiment

Bernadette misses a key event because she remains under quarantine for possible yellow fe-ver because of drinking out of contami-nated petri dishes.

Children’s programming further features scientists, such as Bill Nye The Science Guy. Steinke et. al ex-amined middle-schoolers’ responses to the scientists in these and other shows using traits such as “intelligence, domi-nance, alone, and respected”

This reinforcing of dominant values, however, becomes more compli-cated with The Big Bang Theory through representations of Bernadette and Amy. In particular, these nuances appear through their discussions of their areas of expertise and their careers, their per-formances of their work, and their exter-nal recognitions for their achievements.

Roles for female characters in early sitcoms were domestic ones, such as housekeeper and child care-taker as in I Love Lucy (1951–1957), The Brady Bunch (1969–1974), and Leave It to Beaver (1957–1963).

The Big Bang Theoryseems progressive in that it represents female scientists alongside male scien-tists in ways that value their intelligence and professional achievements.

These main male charac-ters appear in both work and domestic settings throughout the show. The three main female characters do appear in the work situations at different times, but their locations remain primarily in the domestic ones.

Children’s programming further features scientists, such as Bill Nye The Science Guy. Steinke et. al ex-amined middle-schoolers’ responses to the scientists in these and other shows using traits such as “intelligence, domi-nance, alone, and respected” (172) and found the overall response favorable.

Trump had less “fleeting interjections” this debate than the first round, and slightly more interruptions. Clinton had slightly less fleeting interjections, and the same amount of interruptions. The moderators, however, were much more active in this debate than in the first. They interjected (usually to let the candidate know they were running out of time) 41 times throughout the 90 minute debate.

The queue of electronic hands could take so long to get through that some students abandoned hope and lowered their hands while others got into the habit of raising their hand pre-emptively just so they’d have a spot in line if an idea came into their head later on.

Activities such as time spent on task and discussion board interactions are at the forefront of research.

our education system is controlling, exploitative, imperialist

Voyant Tools is a web-based reading and analysis environment for digital texts.

Here's an interesting article about the distinction. 

Crocodoc is a tool that allows annotations on online assignment submissions in Canvas

followed a TAGS Explorer of a conference hashtag

spark even more discussion.

Since its start in 1998, Software Carpentry has evolved from a week-long training course at the US national laboratories into a worldwide volunteer effort to improve researchers' computing skills. This paper explains what we have learned along the way, the challenges we now face, and our plans for the future.

insert reflective pause to acknowledge the power of weak tie networks here

whichoftheavailabletoolswithinasoftwarecanfacilitateyourapproachtoanalysismosteffectively

What is the correlation between levels of student responses to each other and outcomes?

. Human interactional intelligence is, so far as we know, predicated upon five qualities

We conceive this step as devaluation, rather than diffusion, as Schwartz and Merten call it

I personal storie , oldtimers in AA tell their own life stories or partcll them-=Their drinking histories-and how they came to be involved in I AA. These stories contribute to cultural production and reproduction in three ways. First, they objectify many cultural elements-the beliefs, propositions, and interpretations-that new or potential AA members learn through listening. Second, by virtue of their" narrative forms, the stories realize a model of what alcoholism is and what it means to be an alcoholic. This model, in the absence of a well-defined, well-elaborated model shared by the wider culture, provides a basis for potential mem­bers to identify themselves as alcoholics, through comparing their lives to those in the stories. The storyline also provides a basis for labeling others, as others compare the lives of suspected alcoholics to the AA lives. Third, the AA story is a tool of subjectivity, a �p.ediat:ing-.de¥-iG€ for s�standing: As the AA member learns the AA story model, by listening to and telling stories, and comes to place the events and experi­ences of his own··· life into the model, he learns to understand his own�l.ife1 as an AA life, and himself as an AA alcoholic. The .l'ersonal_st"l}'_!s_a cultural vehicle for identity formation.

AA mem­bers knew that I was attending meetings as part of my research, what was said at those meetings was intended for other members, not for the anthropologist, and much was sensitive in nature and private.

This is why, as members often say, "AA is for those who want it, not for those who need it." AA members must agree to become tellers, as well as listeners, of AA stories.

As a cultural system, and one that no one is born into, this entire figured world of AA is new to neophytes.

There are therefore two aspects important to membership in AA: qualification as an alcoholic, based on ones past, and continued non-drinking behavior, or effort at not drinking, which is a . ne ation of the behavior that first qualified one for membership.J

The drinker must apply them to his own life, and this application must be demonstrated

What happens when an AA member fails to compose this new under­standing of himself and of his life?

He does not figure his life in AP!s terms. He views AA as a measure to take when things get really bad. He does not share the set of values and distinctions that unites other AA members. The identity of "alcoholic" does not affect his actions, or his perceptions of self, beyond his drinking behavior.

We believe this key transition that occurs in both schemes is best recast as identification-the formation of a concept of self as an actor in the system.

nli.e less expert women tended to repeat the words and follow the direc-ons of others. They had less of an overview of romantic relationships; hey had to work harder to come up with responses to romantic situ-1 ations. Not surprisingly, those who were less identified with the world of romance, and for whom it was less salient, also were less expert in / JP.anaging relationships.

Talk about men, focus on men, and orientation toward romantic relationships correlated positively with how much the women talked about and treated themselves as ac-tors in the world of romance.

Knowledgeability about the types of men and the ways relationships worked was more or less assumed. Further-level of competence in the conduct of relationships was presumed.

Both "getting the upper hand" and "keeping ·one man up front" were strategies for achieving the valued outcomes of romantic involvements while avoiding the bad.

This suggests that involvement-the salience of and identification with the cultural system of romance-codeveloped with expertise.

Those who ap-peared to be less knowledgeable or less expert closely copied and took direction from others, attended to relatively circumscribed aspects of relationships, and had difficulty generating possible responses to roman-tic situations.

Even though the women were bombarded with images of themselves in the world of romance, and even though many of their peers seemed to have sorted through these various interpretations and arrived at fairly stable views of themselves as actors in the romantic world, some of the women did not identify themselves as such. They had no clear idea of a "romantic" self-either a self to avoid or a self to realize.

uch romantic attach-ments became markedly less salient for her, and her identity as an attrac-tive woman in the world of romance, as culturally construed, became unimportant.

American culture does not generally treat romantic relationships as an area of expertise. q./J -}:f. romantic relationships as something orirrexpert:I.:ove about fatalistically, as somethiilg .• successful relationships were more to_ch'!mft<:.rJiaws, b,Jck, or mismatches of interesiStllanto a lack of skill or savoir Nonetheless, upoii-quesi!Oii.5';)(;,xpertlseaiia

Coach J engagedconversations that fostered social relationships to sustain their effort in a difficultmoment As relationships were built, runners repeated important aspects of thepractice that allow them to gain competence.

lt. Discourse (or discursive) theory emphasizes many of the aspects of cultural resources that we discu

a frame becomes a world-a space

Why is it confusing to ask if the Pope is a bachelor? After all, a bachelor is an unmarried man and the Pope is an unmarried man. Yet there is something peculiar about referring to the Pope as a bachelor. The problem is that "'bachelor' frames ...

Asking if the Pope is a bachelor is akin to trying to redeem one's poker chips for money at an AA meeting. The questioner and the would-be redeemer have both mistaken the relevant figured world.

They come to name themselves, and often to see theruselves, as "alcoholics" and not just drinkers. All these elements of AA are meaningful in, relevant to, and valued not) in relation to a frame of meaning, a virtual world, a world that has been figured.

anterior cingulate area 24

caudalanteriorcingulate

Anterior Cingulate Gyrus

cingulate gyrus

Anterior cingulate cortex

Anterior cingulate area

Anterior cingulate area(ACA)

anterior cingulate cortex

anterior cingulate cortex

anterior cingulate cortex

cingulate cortex (BA24)

area 24 of cingulate cortex, 24

Anterior (rostral) cingulate

Rostral anterior cingulate gyrus

Anterior rostral cingulate cortex

Anterior Cingulate Gyrus

acc

anterior cingulate

anterior cingulate cortex

Anterior cingulate cortex

Anterior cingulate cortex;

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deterministic

In the final analysis, intellectual property shares much of the origins and orientation of all forms of property. At the same time, however, it is a more neutral institution than other forms of property: its limited scope and duration tend to prevent the very accumulation of wealth that Burke championed.

The testimony makes it manifest that he was a special police officer to some extent identified with the work of the prosecutor's office, and that position, upon well-settled grounds of public policy, required him to assist, at least, in the prosecution of offenders against the law. The services he rendered, in this instance, must be presumed to have been rendered in pursuance of that public duty, and for its performance he was not entitled to receive a special quid pro quo.

The results of the subsequent mathematical analysis can often be exported as additional rows and columns into an updated version of the atlas and then explored by the biologist using the visualization tool.

Once a searchable atlas has been constructed there are fundamentally two approaches that can be used to analyze the data: one visual, the other mathematical.

Like any other discipline, the theory of invention and arrangement must be practiced in two ways: first, in order that by its means we should through external examples learn common sense from argument, judgment from the manner of conclusion, and complete prudence from the method of arrangement and order; secondly, that by means of the same art we should devise similar examples in speech and writing.