eCAT: Online Electronic Lab Notebook For Scientific Research

Nigel H Goddard , Rory Macneil and Jonathan Ritchie / Automated Experimentation / 2009 /  1:4  / doi:10.1186 /1759-4499-1-4 /  Published: 29 October 2009

Abstract (provisional)

Background

eCAT is an electronic lab notebook (ELN) developed by Axiope Limited.

[http://www.axiope.com/electronic_lab_notebook_index.html]

It is the first online ELN, the first ELN to be developed in close collaboration with lab scientists, and the first ELN to be targeted at researchers in non-commercial institutions. eCAT was developed in response to feedback from users of a predecessor product. By late 2006 the basic concept had been clarified: a highly scalable web-based collaboration tool that possessed the basic capabilities of commercial ELNs, i.e. a permissions system, controlled sharing, an audit trail, electronic signature and search, and a front end that looked like the electronic counterpart to a paper notebook.

Results

During the development of the beta version feedback was incorporated from many groups including the FDA's Center for Biologics Evaluation & Research, Uppsala University, Children's Hospital Boston, Alex Swarbrick's lab at the Garvan Institute in Sydney and Martin Spitaler at Imperial College. More than 100 individuals and groups worldwide then participated in the beta testing between September 2008 and June 2009. The generally positive response is reflected in the following quote about how one lab is making use of eCAT: "Everyone uses it as an electronic notebook, so they can compile the diverse collections of data that we generate as biologists, such as images and spreadsheets. We use to it to take minutes of meetings. We also use it to manage our common stocks of antibodies, plasmids and so on. Finally, perhaps the most important feature for us is the ability to link records, reagents and experiments."

Conclusions

By developing eCAT in close collaboration with lab scientists, Axiope has come up with a practical and easy to use product that meets the need of scientists to manage, store and share data online. eCAT is already being perceived as a product that labs can continue to use as their data management and sharing grows in scale and complexity.

The complete article is [now] available as a provisional PDF

[http://www.aejournal.net/content/pdf/1759-4499-1-4.pdf]

The fully formatted PDF and HTML versions are in production [10-29-09]

Source

[http://www.aejournal.net/content/1/1/4]

!!! Thanks To / Garrett Eastman / Librarian / Rowland Institute at Harvard / For The HeadsUp !!!

Republicans Wear Sneakers, Too

In 1990, Democratic challenger Harvey Gantt opposed Republican incumbent Jessie Helms in North Carolina's Senate race. Gantt, an early civil rights leader and Mayor of Charlotte, ultimately lost the election, thanks in part to a racially charged advertisement from the Helms campaign. The now infamous ad, “Hands,” depicted a white man crinkling up a piece of paper after losing his job to a minority, implying, of course, that unfair racial quotas were to blame. Written by Republican strategist Alex Castellanos, the ad would go down in political history as one of the more egregious (and successful) exploitations of white resentment for political gain.

When asked to endorse Gantt for the Senate seat, NBA legend and North Carolina native Michael Jordan refused, stating, “Republicans wear sneakers, too.” The implication was clear, and the message came through loudly: As an avid businessman and superstar athlete, Jordan was happy to shelve his politics—and self dignity, for that matter—in favor of merchandise sales.

Flash forward nineteen years. Last week, conservative radio personality and former ESPN NFL commentator Rush Limbaugh announced interest in buying the beleaguered St. Louis Rams. Rejecting Michael Jordan-style political ambivalence, players across the league openly expressed dissatisfaction. Mathias Kiwanuka of the New York Giants, for example, was quoted as saying:

"I mean, I don't want anything to do with a team that he has any part of. He can do whatever he wants, it is a free country. But if it goes through, I can tell you where I am not going to play […] I am not going to draw a conclusion from a person off of one comment, but when it is time after time after time and there's a consistent pattern of disrespect and just a complete misunderstanding of an entire culture that I am a part of, I can't respect him as a man."

Kiwunaka was not alone. In 2003, Limbaugh resigned as an ESPN commentator after making racially charged remarks about Donovan McNabb, suggesting that the Pro Bowl quarterback only reached stardom due to the media’s irrational desire for “a black quarterback [to] do well.” Current players, like New York Jets linebacker Bart Scott, have not forgotten these statements:

“It’s an oxymoron that he criticized Donovan McNabb. A lot of us took it as more of a racial-type thing. I can only imagine how his players would feel. I know I wouldn’t want to play for him. He’s a jerk. He’s an —. What he said (about McNabb) was inappropriate and insensitive, totally off-base. He could offer me whatever he wanted, I wouldn’t play for him. … I wouldn’t play for Rush Limbaugh. My principles are greater and I can’t be bought.”

In a league that’s between 60 and 70 per cent black, it’s more than a little insulting to imagine a man that once suggested the NFL “all too often looks like a game between the Bloods and the Crips without any weapons” could become a team owner. In fact, it’s absolutely outrageous. That a man with such overt, explicit contempt for African Americans could purchase and control an organization that profits from the labor of black athletes signals far too much historical baggage to be appropriate. Sports hold a special, unifying place in American culture, and as a result shouldn’t be a venue that rewards bigotry and divisiveness. Limbaugh’s disrespect of the league, its players, and African Americans in general are all legitimate grounds to oppose his involvement with the NFL—all opinions, I might add, that exist above and beyond any objection to his political views.

Given Limbaugh’s long history of racially charged remarks, it’s not surprising that players were offended by his announcement. But what is surprising is the public nature of their comments. Normally, team owners work to thwart political activism and diffuse dissent among their players. Bad for business, per the Jordan model of merchandise sales. But with the controversy over Limbaugh’s announcement, professional athletes may be moving toward a new model of political discourse, rejecting the Jordan template and re-embracing self dignity. The recent news that Limbaugh was officially dropped from the group bidding to buy the Rams only underscores the potential power of civically engaged professional athletes. Maybe this is the dawn of a new era—an era of renewed self-respect, moral integrity and civic engagement—in professional sports.

Tony Kornheiser of ESPN’s Pardon the Interruption made this very point earlier in the week, suggesting, “We are out of the Michael Jordan era where everyone wears sneakers, and back to the Jim Brown era of social activism.”

No complaints here.

Come Out, Come Out Whoever You Are(?): Outings in Popular Media

To be upfront about this post, it is a response to Bryan Safi’s video That’s Gay: Coming Out. Upon a cursory viewing of the video, one does get a sense of how coming out on popular shows has been constructed in a way to amp up the drama. On this point, I agree. In his comical framing and colorful presentation, however, I question if he does just as much of a disservice to coming out, or rather the choice/experience of coming out, by his depiction of the examples he uses. I will only say two brief points that I believe are overlooked in his “analysis.” And it must be noted that both points grapple with the same question: what about the nonmoments?

To begin, I quote one contributor over at Womanist Musings, the blog where I found this clip. She states that

Once again, [Safi] is so bang on correct. The way that coming out is constructed in the media is absolutely ridiculous. I mean seriously…they make it seem like someone is admitting to murder. Heaven forbid the media just have GLBT people going on with their lives just like everyone else. Oh no, we cannot possible portray being gay or lesbian as anything other than an oddity.

However, I wonder if the contributor to Womanist Musing listened/watched the entire clip. Safi mentions that there has been a proliferation of “outings,” both voluntary and involuntary, in recent history in the media (in this case speaking only to TV sitcoms). He states that “coming out” has been depicted in a number of ways and through various avenues and the like. In fact he outlines, again in a colorful manner, some himself. The question I have is, does this not speak to reality more than fiction? Is it a sign of times getting better and not worse? Though Safi doesn’t include clips from Grey’s Anatomy, for instance, there was an occasion with Cali where the more fanatical, hysterical “outing” didn’t happen. To use one example Safi uses himself, Glee, wasn’t Kurt’s coming out—both to Mercedes and his father—one of the modal occurrences? What about Calvin in Greek: Ashleigh thinking Calvin is hitting on her and she makes a move (a kiss) only to be stopped with the news that he is gay? I am not saying that this is in fact how everyone who is outwardly gay came out, but Safi’s portrayal, at least to me, sullies and minimizes those experiences.

Though I agree that “coming out” has been incorporated into scripts to draw in the crowds, I have to ask about the assumption that we are making about the entire cast of characters being heterosexual save for those who will be somehow marked as gay. I know that some will say this is a statistical fact; there are more heterosexual individuals than homosexual. This may very well be the case but we still see instances in popular sitcomes where we are left in surprise when we find out someone is gay and it is not an instance of the “Flaming Kamikaze” or the “Kanye West Swift Kick.” I think about Grant from Greek, a show that Safi himself uses twice as evidence for his producers using coming out as an attraction to lure viewers in. No one on the show knew that Grant, Calvin’s new boyfriend, was gay until he and Calvin started hooking up. It seems to me that from the position Safi puts himself in is one that assumes everyone is straight until proven otherwise. That, to me, is problematic in and of itself though I do understand that given the history of LGBQTI individuals in the media, it is a reasonable assumption.

When speaking of such an important life event in people’s lives I think we have to be a little smarter in our analysis even when trying to be snarky and comical. Sadly, Safi sensationalizes the outings in the same manner he vilifies the media for doing. Is that the pot calling the kettle black? Instead of taking a more exhaustive, panoramic view of the presence of LGBQTI individuals on television shows and their “outings” and lack thereof, Safi lets us all down, gay and straight alike.

What Up?!

Watching the GOP scramble to rebrand their party’s image following President Obama’s election has been a fascinating development in American politics. But nothing has been quite as interesting as the GOP’s new website, launched yesterday, aptly found at GOP.com. In a dramatic push to make the Party appear more inclusive, the site depicts a wide range of “Faces of the GOP”—not surprisingly composed primarily of women and racial minorities.

RNC Chairman Michael Steele runs his own blog on the site, originally titled “What Up,” but later changed to “Change the Game” following ridicule from folks on the Left. Steele used his first blog post to laud the Internet’s mobilizing potential and prompt readers with the age-old question, “What makes you a Republican?” Judging from the Party’s current organizational schizophrenia, I can only imagine the range of responses Steele’s going to get.

Still, Steele’s efforts are admirable, if a little suspect. He really is committed to “changing the game,” making the GOP more inclusive in an era of multiculturalism and diversity. And GOP.com is a much better effort than Steele’s last push to attract more diversity to the Republican Party. When asked a few months back how he plans to bring more minorities to the GOP, Steele replied, “My plan is to say, ‘Ya’ll come.’” A member of the audience then shouted, “I’ll bring the collard greens,” to which Steele added, “I got the fried chicken and potato salad.” There’s no fried chicken recipes at GOP.com, but there certainly are many pictures of black faces sprinkled throughout the website. Dropping the racial stereotypes in favor of symbolic inclusion is, at the very least, a step forward for the GOP.

That said, it’s an understatement to interpret the site as a feigned, superficial attempt to promote racial diversity within a Party that still supports policies of racial inequality. It feels forced, to say the least. The fact that the website lacks a Spanish language conversion option only adds credence to its symbolic—rather than material, substantive, or tangible—purpose. We are talking about a Party with a long, storied history of racialized politics, after all. You know, the same Party that coined the term “welfare queens,” used Willie Horton for political advantage, and sent around emails depicting President Obama as a witch doctor with a bone through his nose. Yeah, that shining Party of racial inclusion.

It is at GOP.com that we truly see race, politics, and racial politics collide and intersect. Steele—the first black Chairman of the RNC—is desperately trying to respond to America’s changing demographics, pandering to a slice of the electorate that, at least in part, affected the outcome of last November’s historic election. That folks (often from the Left) are questioning Steele’s blackness only emphasizes the infusion of race in American politics. And it’s not just “racial politics” at play—you know, politicians catering to different racial groups—but an example of how race and racial considerations inform political messages and campaigns. Race is omnipresent in American politics, just as it is omnipresent in American culture. The content of GOP.com illustrates the political imperative of racial inclusion, but it’s difficult to imagine how the Party can reconcile this lofty goal with the politics of white resentment that has historically formed the Party’s base. Factor in Steele’s racial identity, and the RNC emerges as a social laboratory of racial dynamics, balancing multiculturalism with implicit racism and operating within the context of our nation’s first multi-racial President. Symbolic gesture or not, GOP.com is a window into a layered world of race and politics.

It’s unclear how Americans, minority or otherwise, will react to GOP.com. There are, indeed, plenty of racial minorities that believe in limited government, states’ rights, and many other aspects of the Republican Party’s platform. But I imagine it’s hard to get on board with a Party that fans the flames of racial resentment for political gain. Will GOP.com “change the game?” Maybe, but it will be an uphill battle for the RNC. Unfortunately for Steele, a few black and brown faces on a website—the same site that beckons minorities by asking “What Up?!”—can’t exactly make up for decades of racial animus and exclusionary policies. The RNC’s racial conundrum may ultimately prove too difficult to overcome.

More on Obama & Gay Rights

Yesterday's post on Obama and gay rights deserves an addendum following Jamelle's insightful critique over at The League of Ordinary Gentlemen. On the whole, I think Jamelle makes some important points about social equality and politics.

To wit:

President Bush, if you remember, supported a Federal Marriage Amendment to the Constitution, and was generally supportive of state-based efforts to strip gay Americans of their rights. Indeed, stoking fear and hostility towards gay Americans was part of the Bush administration’s reelection effort. I mean, to just sort of underscore the degree to which it was open season on gay Americans, the White House consistently opposed the extension of hate crimes legislation to gays, even as the country saw a sharp rise in the number of hate crimes targeted at gays. Activists are well within their rights to criticize Obama’s speech as “just words,” but in doing so, they miss an important fact about presidential rhetoric: it makes a difference. It further brings gay concerns into the mainstream and gives them a sense of urgency.

This is certainly not to say that the gay community should ignore the fact that Obama has yet to really move on gay rights, but on the whole, I that it’s far more productive to at least acknowledge that Barack Obama is an ally, and – slow-walking notwithstanding – is openly supportive of gay rights. Tearing him down politically – as opposed to lobbying and pressuring – only makes his job that much harder.

Presidential rhetoric, though largely symbolic, definitely makes a difference. America's general disdain for identity politics often makes such rhetoric politically damaging, so going out on a limb for gay rights is certainly commendable. Attacks levied against President Obama, as Jamelle notes, do in fact lack historical perspective, as the last eight years were pretty atrocious as far as civil liberties and social equality are concerned.

That said, I think much of the defense of Obama on this issue also lacks perspective. I doubt many Obama defenders wake up each morning to a partner they can't call "husband" or "wife" because of some laughable "sanctity" of marriage. I doubt many people arguing "Just wait, your time will come" have to suppress their identity among men and women they share the ultimate wartime bond with. I doubt many people ignorantly claiming "Congress will defend gay rights when they have time" live with an identity that's caricatured in pop culture and historically rejected as immoral and perverse. I doubt many people suggesting "He's done a lot for gay rights already" face a culture where accepting your sexual identity is referred to as "coming out"--suggesting that your very existence represents a rejection of social norms. In judging a President's record on social equality, this is the perspective we need to keep in mind. This perspective--the human element behind the politics of social policy--is, in my opinion, a critical measure of our progress as a nation. And it is within this context that many critics are (rightfully) a bit frustrated with the Obama administration.

But Jamelle's also right: There's a fine line between attacking President Obama on this issue and pressuring him to move forward with his promises. Political criticism, when done tactfully, is healthy--but criticism can very quickly become an unhelpful attack. Obama's symbolic gestures are magnanimous, yes, but most of us can agree there's still a long way to go.

Meghan McCain Continues to Impress, President Obama Continues to Disappoint

Fresh off his Nobel Peace Prize announcement, President Obama addressed thousands of gay right protestors marching at our nation’s capital this past Saturday night. It was a rousing speech, as always, filled with promises and strong, assertive language.

But it was an empty speech, void of action, conviction, or credibility. He promised to repeal “Don’t Ask, Don’t Tell,” the controversial Clinton-era policy of identity suppression in the military. But it was a promise he’d made before. And it was a promise he has thus far utterly failed to act upon.

As Andrew Sullivan writes:

All I can say is: the president gave a speech he could have given at any point in the last three years. No one in that room could disagree with any of the things he said. I sure don't (with the exception of the hate crimes hooey). And he said it well and movingly. Like we didn't know he could do that.

But the point of electing a president who pledged to actually do things is to hold him to account, and to see if he is willing to take any risk of any kind to actually do something. I had a few prior tests of his seriousness or signs that he gets it, a few ways to judge if this speech had anything new or specific or clear. He failed every test.

Meghan McCain, equally appalled, writes:

Obama offered no timeline for phasing out this policy and, as usual, no real specifics. But the president verbalized his commitment to ending it—which is not insignificant [...]During the election, Obama pledged that the very first thing he would do as president would be to repeal Don't Ask, Don't Tell. Although I thought it was an ambitious promise, I believed him. It's now almost a year into his presidency and other than making speeches, nothing has happened.

There’s no two ways around it: Sullivan and McCain are spot on. This administration has thus far been absolutely abysmal in promoting social equality. Abysmal. Crumbling economy notwithstanding, don’t get on a pulpit and expect us to be happy with negligence. Don’t say all the right things and expect us to be satisfied with gross inaction. Don’t try to appease the progressive electorate that struggled to put you in office. Don’t make empty promises you have no intention of honoring.

It’s a sad state of affairs when the daughter of Obama’s Republican challenger from last November has a better stance on gay rights than our own Democratic President. If the Nobel Peace Price was intended to push Obama to, you know, actually promote peace by ending our two wars, what award do we need to give him to promote gay rights? What will it take, and how much longer must we wait?

As Meghan McCain continues to assert herself at the forefront of the fight for gay rights, Obama continues to disappoint. Maybe he thinks repealing "Don’t Ask, Don’t Tell" is unwise politically, regardless of his personal beliefs. Maybe he thinks a gay rights agenda will hurt him in the future. This may be so, but his insulting failure to act—on the eve of National Coming Out Day, no less—certainly isn’t winning him any new progressive allies.

Obama has the potential to promote real, substantive change. Unfortunately, it doesn't look like he'll be acting on that potential any time soon.