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[Note: It appears that SharePoint magazine has bitten the dust and with it went my old series on the "tribute to the humble leave form". I am still getting requests to a) finish it and b) republish it. So I am reposting it to here on cleverworkarounds. If you have not seen this before, bear in mind it was first published in 2008.]Hi all
Welcome to edition 7 of this seemingly never-ending tribute to the humble annual leave (vacation) form. This is getting to be like the "Friday the 13th" series of movies – they never stop!
First up, I want to categorically state that, as a heterosexual Australian male, I have a few stereotypical personality traits . I enjoy beer, kung-fu movies, Burger Rings, Vegemite and Tim-Tams, love the cricket (especially playing India) and most importantly of all, I do not read instructions. Period. I think that ignoring the RTFM rule is a characteristic of all of humanity but Australians in particular seem to celebrate this trait as something endearing.
Therefore, it pains me greatly to have to inform you that this seventh edition of the series is one of those posts where you have to put on the brakes and explain some really boring conceptual stuff to proceed with the rest of the series. Yeah, I know – theory is boring and sucky and you just wanna get into the nuts and bolts of it all. But, as Homer demonstrates below, sometimes we have to defy our genetic programming and actually read the instructions. The alternative is a SharePoint solution equivalent to that of Homers BBQ.
This post will deal with some of the mechanics of form submission and form publishing.
What has gone before…
The first few posts in this series are starting to get hazy – it seems so long ago now. To sum it all up in a nutshell, we introduced the leave form as a means to introduce a lot of key SharePoint features in an easy to understand and relevant way. We set several requirements that we had to achieve.
- Automatic identification of requestor
- Reduce data entry
- Validation of dates, specifically the automatic calculation of days absent (excluding weekends)
- Mr Burns is not the only approver, we will need the workflow to route the leave approval to the right supervisor
- We have a central leave calendar to update
At the end of part 6 we were working on validation of dates. We added some validation rules to ensure that you could not return to work before you started your leave of absence. But at the end of that post, I showed how a published form did not obey our data validation rule, where the form was set to prohibit incorrect dates, yet I was able to click save and put the form straight into the document library. What the…?Why did this occur?
Saving vs Submitting – form confusion
Like everything else designed by nerdy engineers, InfoPath and Forms Services can be used in a few different ways. This offers flexibility of course, but has the disadvantage that if the flexibility is not well understood (i.e not reading the instructions ), it is easy to cause user confusion. Homer is a classic case of a person who, when faced with two choices, will always pick the wrong one.
You have to remember that InfoPath started out as a program installed onto your PC, along with other MSOffice applications. Thus, historically, an InfoPath form is just another type of document. In its simplest (and default) scenario, the form is very much like any other MSOffice document in that you create/open the form, edit it and then save it.
But hang on a second! Most of the time, the data collected in the form is part of a larger business process. Also most of the time, business process needs to do "stuff" with the information that the user has entered. In other words, the data usually doesn't stay in the forms that users fill out.
So the InfoPath designers, wanting to please everybody, designed InfoPath in such a way that saving a form and submitting a form are two different things. Homer Simpson doesn't care about this nor should he. He just wants to fill out the form so he can go back to dreaming about the land of chocolate.
Here is the key thing you need to know, though. Saving a form is, in effect, performed on the presumption that the form is still a work in progress. Saving the form should be thought about in the same way you would save a word document after performing some edits. Because the form is still a work in progress, data validation should not take place.
But at some point the form stops being a 'document' and becomes…well… a form! It is complete and no more edits should be made. This is when you actually submit the form!
Submitting a form triggers the data validation rules that were set up in part 6.
Big deal…When does this get hard, Paul?
Okay, so you may not think that there is really that much of a drama with the whole "save vs submit" thing. But when InfoPath is integrated with SharePoint via Forms Services, it can get complicated. You see, InfoPath allows you to create forms that submit their data to one or more locations. For example, the Springfield Nuclear Power Plant leave form could be set up so that when Homer submits his application, the data is sent to a database, and a copy of each completed form is also sent in an e-mail message to Waylon Smithers and Monty Burns.
For reference, here are the places that InfoPath can submit to;
- A Microsoft Access or Microsoft SQL Server database
- A Web service
- A server running Microsoft Windows SharePoint Services
- In an e-mail message
- An application on a Web server
- A custom application that hosts InfoPath
Now, given that this series of articles is about SharePoint, which option of the above list do you think we are interested in? You guessed it! The third option in the above list is SharePoint.
But here is the root cause of the confusion, when you publish an InfoPath form to SharePoint, all forms that you fill in end up being created in a document library. Back in part 4 of this series, we first published the form and as part of that process, created a form library called "Leave Forms". Consider the screenshot below. We are about to create a new form in this library.
Below is a screenshot of the new form to fill out. Note the toolbar at the top with a "Save" and "Save As" options. If you then click 'Save" on the form, it will prompt you to save into the above document library.
Therefore, if you use the "Save" option, the "In-progress" copies of the form are stored in the document library and no data validation has taken place. You really have not submitted the form at all.
Does the end user realise this? Some might – but come on! This is Homer J Simpson we are talking about here!
So clearly we need to submit this form because in part 6 we added validation rules that need to be checked. But, what the…? – How the hell do I submit?
Setting up form submission
Real programmer disclaimer: Yes I know there are other ways of doing all of this, but remember – this series of posts is for beginners.
Okay, for now the theory bit is over, and now we get to play with InfoPath again. We are going to add the form submission capability to our existing form so that we can actually submit the form. The thing is, I am also going to *remove* the "Save" and "Save As" options from that toolbar, so that the only action you can make is to submit.
Why would I do this? Several reasons.
- It is a simple form and really, you either fill it in and submit or you don't. There really isn't that much of an imperative to save this form, prior to submitting it.
- When you submit a form, and you are submitting to a SharePoint library, the submitted form is saved. Therefore, I don't need a "work in progress" copy.
- The Homer factor. If you supply a "Submit" and a "Save" button, you know full well that Homer will go and click the "Save" button, when he should be clicking "Submit". As soon as the save dialog pops up, he won't know what to do. At this point he will lose interest and fall asleep.
Hiding save buttons
So, start InfoPath, open up the leave form in design mode, and choose "Form options" from the "Tools" menu.
From the list of options, choose "Open and Save" and uncheck the "Save and Save As" checkbox as shown below.
Click "OK" and republish this form to SharePoint using the steps described in part 4. Note the before and after screenshots below
Spot the difference? The "Save" and "Save As" buttons are missing, and with that I can confidently say that I have now made this form Homer proof because he can't inadvertently click "Save" and think he has submitted the form. Of course, it is so Homer proof that he now has no way to submit the form, so now we have to enable the "Submit" button.
Enabling the submit button
Once again, open the leave form in design mode, and choose "Submit Options" from the "Tools" menu. InfoPath will dutifully display a fairly nondescript dialog box that, at first glance, seems rather simple. There is a checkbox that you need to tick to "enable form submission". Sweet! How easy is that?
Upon checking that box, you now have to choose where you are going to send form data to. The default option is "Email", but we want to send it to a SharePoint document library, as shown below. Choose SharePoint and then click OK.
Uh oh! Did I say this was going to be easy? Okay I lied .
So, what is this message telling us? "You must select a data connection for submitting to a SharePoint document library". Hmmm…I hope that something about that message sounds vaguely familiar to you. That is because this is not the first time we have dealt with data connections.
Data Connections revisited
Way back in part 5, you earned your CCLFD certification by creating a data source that automatically identified Homer by talking to SharePoint web services. If you missed that post, then I suggest reading it, as it is a great example of utilising data connections to *receive* data into InfoPath.
In part 5, we set up a data connection to a webservice by following a wizard. To remind you of how it was done, I have copied the screenshots to this post.
Now, take a look at the second screenshot from the above three. It is asking you to create a connection to receive or submit data and at that time we were receiving data. Guess which one we are doing this time?
So, back to our "Submit Options" dialog box. We were not able to click "OK", because we have not created a data connection to submit the data. Let's now start this process by clicking the "Add" button. Given that you have already told SharePoint that you want to submit to a document library, InfoPath now wants to know the name of that document library and the name of the file that will be created by the submit.
Now, given that the entire staff of the nuclear power plant will be filling out this form, we don't want to simply call the submitted form "Form" as suggested by default. If we did that, we would end up with a document library containing a single file called "FORM" due to the fact that all previous "FORM" files would have been overwritten and replaced by the current "FORM".
Luckily the InfoPath team anticipated this and the filename can be dynamically generated using functions. (We looked at functions early in part 5).
First up though, I will specify the document library to submit completed forms to. It will be in the same document library that we was created when we first published the leave form in part 4,the imaginatively titled "Leave Forms". Below is the library as it is inside the radiactivenet site. Note the URL is exactly what I entered into the "Document Library" field.
A unique filename
The final step for submission is to create an auto-generated filename that is unique. Although the principle is dead simple, this bit is actually tricky when you do it for the first time.
The file naming convention to be used will be as follows:
"Leave Form – " + [EmployeeName field] + " – ", [LeaveType field] + " – " + [todays date]
Here are some examples of this convention in action with various staff.
- "Leave Form – Homer Simpson – Sick – 2007-09-18″
- "Leave Form – Lenny Leonard – Annual – 2008-11-22″
- "Leave Form – Carl Carlson – Bereavement – 2008-12-25″
So, how do we achieve this? Let's get back to the screen where we are prompted to add a file name for a submitted form.
Click the "Fx" button to the right of the "File name" textbox and you will be presented with the (far too small to be user friendly) "Insert Formula" dialog box. We are going to create a formula that constructs the desired file name.
The first thing to note is that we will be using a combination of fixed text, the data entered on the form and built in InfoPath functions. To join all these together in the manner we want is referred to as concatenation. Why do people call it concatenation? I have no idea but it's obvious that an engineer thought up that name! .
We start by inserting the concatenation function called "concat". Click "Insert Function" and in the leftmost window choose the "Text" category. The function called "concat" should be the first one listed. Select it and click "OK' and you will see that a partially completed formula has been created.
The first part of our file name is the text "Leave Form – ". So single click the first occurrence of the "double click to insert field" hyperlink and it will be highlighted. From here, simply type in the string "Leave Form – " (including the double quotes).
The next part of the file name is the name of the employee. We already have this, because in part 5 we set up a data connection to automagically grab first name and surname and store it in the textbox called "EmployeeName".
Single click the next occurrence of the "double click to insert field" hyperlink and it will be highlighted. From here, click "Insert Field or Group" and choose "EmployeeName" from the list of fields.
Okay, so we have the "Leave Form – Homer Simpson" part done. Next we want a hyphen " – " and then the LeaveType field. By now you should be getting familiar editing the formula in the dialog box. Rather than bore you with even more screenshots, I'll talk through the next 2 steps.
- Single click the next "double click to insert field" link.
- Type in (note the leading and trailing space) " – "
- Type in a comma (minus quotes) ","
- Click "Insert Field or Group" button
- Choose the "LeaveType" field and click OK.
If all has gone to the script, then you will see this in for formula box.
Note that you can use the mouse to place the cursor anywhere in the Formula textbox and modify what is there.
Finally, we need another hyphen and to insert another function. This time the function is called "time" and it returns the current date in a short locale based format.
- Referring to the above screenshot, place your cursor between the last letter of the underlined LeaveType (which is "e" ) and the closing bracket.
- Type in (including the quotes and note the leading and trailing space) " – "
- Type in a comma (minus quotes) ","
- Click "Insert Function" button
- Choose "Date and Time" from the Categories List in the "Insert Function" dialog box
- Choose "today" from the list of functions and click "OK"
We are done! The final formula looks like this. Click "OK" and you now should be back at the data connection wizard (the second screenshot below).
Click "NEXT" on the wizard, and we are prompted to give this data connection a name. Since this data connection has been created to submit leave forms to a document library called "Leave Forms", I figured that a good name would be "Submit to Leave Form Library". Click "Finish" and you are done!
To recap on what we have completed in this section, each time a form is submitted, its filename will be automatically specified and the end-user does not have to worry about it.
All rightie, then! Let's republish this form to SharePoint and take a look at the effect.
Testing it out
Assuming everything worked, the effect of what we have done is immediately noticeable. We now have a "Submit" button on the form where the "Save" and "Save As" used to be. Sweet!
So let's test the data validation rules that we created in part 6. If you recall, this form should not be submitted if the return date is before the start date. For that to really happen you would have to be Dr Who and use the Tardis to arrive before your departure…
Below is the form with deliberately incorrect data (click to enlarge).
If I now click the newly visible "Submit" button, what happens? Ecccccxcelent! It refuses to submit the form.
I don't know about you, but this is one of those error messages that some people simply will not read. Homer will no doubt call technical support but the point is, crap data has not gotten past the form in the first place.
Now, when we correct the fault and resubmit the form, it accepts!
Click "Close" and we now see the newly submitted form in the document library, saved with our file naming convention! Woohoo!
Conclusion (Are we done yet?)
We now have achieved the goal of ensuring that our form is validated before being submitted. From a skills point of view, you now have created data connections to both send and receive data and you have integrated your form with web services, as well as some nice data validation logic.
Waylon Smithers is still pleased with progress thus far, and Homer hasn't managed to completely derail things just yet.
But unfortunately for all of us, there is still much work to do. The next post will spend some time pimping up this whole validation and submission process, illustrating a pitfall or two along the way.
Thanks for reading
[Note: I never finished this series for various reasons. I hope that these 7 posts helps you nonetheless]
Paul Culmsee


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We saw burly great skuas powering their way through the stiff breeze. Snow-white gannets sliced the air and tickled the waves with their wingtips. Pilot whales appeared from the depths, a jet of spray came from a sperm whale and a pod of common dolphins joined us to surf our bow wave!
I saw lots of new and fascinating things in the Bay of Biscay. My favourites were the great shearwaters - relatives of the albatross family which breed in the South Atlantic - which flew just above the waves with such skill and certainty. The pod of more than 100 common dolphins which burst through the waves was a pretty amazing sight, too...!
We couldn't help but be impressed by the whales, dolphins and seabirds that we saw. Way out of sight of land, they were in their element and wonderfully adapted to deal with whatever the ocean threw at them. Even the storm petrels - tiny seabirds not much bigger than a sparrow - were right at home among the heaving waves.
Perhaps oddly, there were other creatures out at sea which impressed me more. Things you might not expect...
We had stowaways. While we watched for sealife from the deck of the ferry, more passengers came to rest onboard. Robins.
You've got to ask yourself: why does a robin want to cross the Bay of Biscay? We're not talking about just popping over the Channel... some of the birds were a hundred miles from land. They fluttered alongside the boat and found nooks and crannies to hide in, some in the lifeboats, which seemed entirely appropriate.
Most robins from the UK stay in Blighty, but a few have been found in France, Spain and Portugal during winter. It's likely that the birds I saw originated from mainland Europe - perhaps Scandinavia, from where robins and other thrushes will be arriving on the UK's east coast very soon. However, you really would think that it would be more sensible to fly over land!
There were other birds too, including a redstart, song thrush, a few swallows and meadow pipits. A chiffchaff joined us for part of the trip and there was even a migrant marmalade hoverfly for a while!
But it was the robins which stole my heart. Never underestimate a robin...
I love to make the most of the weekend. Don't get me wrong, I enjoy working for the RSPB, but you can't beat that feeling of coming in to work on a Monday morning knowing that I got out and about at the weekend, - preferably having been somewhere fabulous and seen something to keep me smiling all week!
My Saturday treats started with the surprise sight of a hunting migrant osprey off the Norfolk Coast.
For 15 minutes, the adult bird (clearly an experienced fisher) patrolled high over the beach before I finally saw it fold its wings and drop like a stone. It came up with a big fish – something tasty and salty no doubt!
There were other migrant birds from far afield around too. Later in the day I was watching a wryneck. This little woodpecker is a beautiful (but indescribable!) combination of bars, stripes and anchor marks. I've posted a picture I took of one last year so you get the idea if you've never seen one!
It was hopping around on some short grass and sidled up to rocks to whip out its long tongue and collect ants hiding in the cracks. It would have almost certainly originated from Scandinavia (they don't nest here) and made landfall overnight on its migration.
The wryneck is one of my favourite birds that I'm lucky to see maybe just once every year.
Walking back, a barn owl was hunting right next to the path and then I noticed the tide had come right in, pushing all the waders off the mudflats and up into the air. I estimated the flocks of knot stretched for almost a quarter of a mile against the setting sun – an incredible sight. That's a lot of birds. I reckoned about 60,000 in total.
Of course this is a great time of year for seeing big numbers of birds.
Lots of birds from garden birds to geese start to form big flocks for winter as the autumn goes on. And keep an eye on your local starling flocks as Russian immigrants join your garden regulars to create big, noisy, swirling flocks. So you don't need to go far to see amazing things this autumn.
Feathers are a marvellous thing. That's what struck me today when I was out walking at The Lodge, in search of our flock of Manx Loghtan sheep (they're the little ones with dead-bracken-coloured wool and up to six horns...).
I was busy not seeing the sheep, who were doubtless hiding in amongst the dead bracken, when I spotted a feather lying on the ground. I was pretty sure it was going to be from a woodpigeon (there are a lot around at the moment), but something prompted me to flip it over with my foot for a closer look.
All was revealed.
I'd stumbled across my holy grail!
When I saw the bright blue patch on one side, I gasped. I'd dreamed of finding one of these, a beautiful feather from a jay's wing. I remember a few years ago, when Mark showed me one he'd found, and feeling distinctly jealous.
Though I don't actively go looking for feathers, I most definitely keep an eye out for them on my travels. I like playing at being a nature detective.
Finding and identifying feathers means you gain a little insight into who's been there and what's been going on. A couple of weeks ago, I found a sad little pile of stripy, khaki-green feathers - some with bloodstaining - that showed a green woodpecker had been eaten, probably by a sparrowhawk. The bad news for the woodpecker meant good news for the hawk. That's how it goes...
I've seen plenty of jays at The Lodge, specially in the autumn months when they're busy flying around looking for acorns and places to stash them. Now, whenever I open the chest of drawers under my desk (where my feather 'collection' lurks), I'll be reminded of those charismatic, elusive birds. I wonder whether the jay that it belonged to is the one that's squawking outside my window now...?

subset: commoncrawl


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Click here to print the obituary below
In Memory of
James R Jeschke
March 8, 1937 - June 28, 2013
James R. Jeschke was born in Everett to Robert (Bob) and Ermintrude (Tudy) Jeschke on March 8, 1937. Jim grew up with his sister Nannet who is now deceased.
Jim graduated from Everett High School in 1955. He attended Everett Community College doing several jobs and some traveling. He joined the Navy as a radioman for two years.
He soon became a member of ILWU Local 32, here in Everett. He served over 40 years before he retired. Some of his duties included being on the local Safety Committee for many years.
He also represented the Washington Area Governors Joint Accident Prevention Committee, which he attended in Olympia for over 25 years.
He always had a passion for traveling, which brought him all over the world. He and Sherry met and were married in 1983, on the island of Kauai. Jim had a timeshare on Maui that they eventually upgraded to a larger unit; mainly to accommodate friends and family.
Jim was a life member of the Everett Elks Lodge #479. He also was a life member of the Everett Eagles Arie #13.
He leaves his loving wife, Sherry; step daughter, Vicki Curtis (Dana); grandson, Kellen; niece, Dennice
(David) Dierreck and their children, Matthew and
Many thanks to cousin Nancy Andes for being so helpful with his many medical difficulties, also, the Puget Sound Kidney Center and All About Care team, Sam King, Karano Bojang, and Cheryl for their excellent care while staying in his home.
A toast will be given in his honor on the 4th of July by the ILWU Local 32.
Arrangement will be made by Cypress Lawn Cemetery. At Jim's request there will be no funeral.
He will always be remembered for his enthusiasm for life. He will also be missed by his many friends as well as his family.


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The University of Southern Mississippi Gulf Coast Civic Chorale will perform its annual tradition of rousing audiences with two holiday concerts on the Mississippi Gulf Coast. The chorale will feature "Magnificat" and the "Song of Mary," along with traditional holiday favorites.
The first performance is scheduled for Friday, Dec. 7, at 7:30 p.m. in the Fleming Education Center auditorium at the Southern Miss Gulf Park campus in Long Beach, Miss. The encore performance is scheduled for Sunday, Dec. 9, at 3 p.m. at St. Michael's Catholic Church in Biloxi, Miss.
The holiday concerts are free and open to the public. Celebrating its 18th year at Southern Miss, the chorale serves as a community outreach program welcoming members of all ages throughout the Mississippi Gulf Coast. Over 80 members sing in the ensemble, which is led by John Flanery, assistant choral director at Southern Miss.
For more information, visit www.usm.edu/gc/civic_chorale or call 228.865.4573.


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ELMIRA, N.Y., July 13.--The Robert A. Packer Hospital, at Sayre, Penn., was formally opened to-day. The hospital was named after the late millionaire and President of the Lehigh Valley Railroad, Robert A. Packer. The building was formerly the residence of Mr. Packer, who requested that after his death the building...
July 14, 1885
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Shannon Chalmers
I enjoy time spent at home with family, watching movies, walking my dogs, and also am working to certify my current dog as a therapy dog. This will be the second dog that I have certified and it is something that I am very passionate about. I enjoy volunteering through local animal rescue organizations as a foster parent, as well.
Education and Professional Experiences
I grew up outside of Pittsburgh, Pennsylvania, and attended Catholic grade and high school. I appreciated having to wear a uniform to school, as it definitely lent to more of a sense of a balanced and equal community. I have a Bachelor of Arts degree in Art History from the University of Pittsburgh, a Master's of Arts in Special Education from the University of Northern Colorado, and a Master's of Education in Humane Education from Cambridge, College. Lifelong learning is very important to me and I truly believe that we are always given opportunities to learn, in every instant, and every environment. I lived in Northern Colorado for over twelve years and it is truly a beautiful, sunny place. I have worked in teaching for over eight years and prior to that, I was a director at a residential treatment facility.
What has been your greatest learning experience? (in or out of school)
My greatest learning experience is simply the realization that learning never ends! I am always constantly learning, shaping, and reshaping my beliefs, as well as my personal and professional skills and abilities.
Who do you admire and why?
At this time, I admire Zoe Weil, who, as head of the Institute for Humane Education, is co-founder of the very first Solutionary School, to be housed in New York City. This school is the first of it's kind, and while there are many premises to this PK-12 school, the most important is that students will be learning, through equal parts of instruction in the arts, physical education, academia, how to serve as change agents in the world. I am very excited to see what unfolds for this school in 2016 and beyond.
What do you love about your current WSD position and the WSD community?
I am honored to work with such amazing teachers and support staff, who are all truly diligent in their methods and approaches in helping to educate the whole child. My students are an incredible group of young women and men who teach me as much as I teach them, every day. It truly feels like a community of learners.


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What does valens, flavius mean?
Definitions for valens, flavius
Here are all the possible meanings and translations of the word valens, flavius.
The Nuttall Encyclopedia
Valens, Flavius
Emperor of the East from 364 to 378; nominated by his brother Valentinian I. emperor of the West; was harassed all his reign by the Goths, who had been allowed to settle in the empire, and whom he drove into revolt, to the defeat of his army in 378, in a battle in which he was himself slain; the controversy between the orthodox and the Arians was at its height in this reign, and to the latter party both he and his victors belonged; b. 328.
Chaldean Numerology
The numerical value of valens, flavius in Chaldean Numerology is: 6
Pythagorean Numerology
The numerical value of valens, flavius in Pythagorean Numerology is: 1
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I totally forgot to post this when it came out about a week after I defended. The folks who run the hilarious video podcast Breaking Bio had me on as their special guest, with Heidi Smith reporting live on location. Check it out:
Category Archives: Open Notebook
The Biophysical Effects of Heavy Water – My Defense Presentation
Defense Outline
Just over a week away now…
- Introduction
- What is D2O?
- The history of D2O
- Gilbert Lewis:
- purification
- biological effects
- The hypothesis
- Joseph Katz
- various experiments
- Gilbert Lewis:
- Uses of D2O
- NMR, mass spec
- The need for a D2O adapted organism
- Experiments in DDW
- use for space travel
- cure for cancer?
- The effects on life
- Tobacco Seeds
- The Crumley experiment and repeating the experiment
- Tobacco seed germination rate
- tobacco seed growth rate in low deuterium concentration
- Arabidopsis
- arabidopsis growth rate
- arabidopsis morphology
- E. coli
- growth rates
- adaptation and adapted growth
- morphology
- Yeast
- growth rates
- adaptation – can't adapt
- morphology
- stall during cell division
- microtubule stabilization in D2O
- Tobacco Seeds
- Molecular effects
- Stabilization of biomacromolecules
- DLS experiments
- Catalase
- Ovalbumin
- YPD longevity
- DLS experiments
- Investigation of HD exchange
- mechanism and exploitation for protein struture studies
- FT-IR analysis
- Cavity ring-down analysis
- low cost measurement of local atmosphere isotopic composition
- Effect on DNA
- The pursuit of shotgun DNA mapping
- optical tweezers
- methods
- overstretching data
- Stabilization of biomacromolecules
- Future Work
- Arabidopsis
- adaptation
- seed growth in low deuterium
- Tobacco growth in low D2O
- Yeast morphology in taxol
- E coli protein expression in D2O and protein structure analysis
- overstretching in D2O with intercalators
- Arabidopsis
Well there is my idea of how to present my dissertation. I'm not sure if/where I should put my discussion on open notebook science. Also there are a couple things that I could see going elsewhere. I could describe the yeast and e. coli stuff in parallel instead of one after another. Also the HD exchange stuff could easily go right after the yeast, e. coli, or even the tobacco seed stuff. What to do…
Otherwise I think the story is pretty compelling: history of D2O and the unanswered question by Lewis. Investigations into D2O effects and trying to understand low D2O concentration effects, effects on macromolecules, and the understanding of large volume/long-term HD exchange.
Any feedback you may have would be GREATLY appreciated. I'll send you a figshare t-shirt, or if you are XL, I'll send you a hoodie (but I only have one).
Chapter 1: Open Notebook Science
View in Google Drive.
The link above should give you access to the chapter in all it's glory. Currently it is pretty much done barring revisions, the addition of figures, and moving the references from side comments to an end of chapter reference section. I'm providing an embed below in case you don't care about all the cool references enclosed and just want to read. If you are reading via mobile, click the link.
The entire story of my scientific career
This article is actually the introduction to my dissertation and I thought I'd share it with the world officially rather than let it die in an electronic archive somewhere. I've shared this story in some form or another several times already, but I've never provided the entire account like this. And so, it is with great pleasure that I share with you, the story of how I became the scientist that I am today…
I joined the KochLab in the Spring of 2007. It was a brand new lab that, at the time, was comprised of Dr. Koch, myself, and my best friend Larry Herskowitz (who is now Dr. Herskowitz). In our first lab meeting, Dr. Koch discussed his scientific endeavors up to that point (some of which are continued in this dissertation) and introduced the concept of open science.
Open science was, and still is, an emerging paradigm, and is not to be confused with a particular field of science. The core concept of open science is providing access information and it is through the opening of scientific research that many new endeavors have become possible. Many of these endeavors have changed the way scientists approach research and acquire data. Citizen science, for instance, has brought a mass scale of human analysis to previously unsolvable problems. Even sharing data has led to new forms of collaboration. Data repositories have allowed scientists to share data with the world in hopes of finding new uses for the shared data. Tools like DataOne have emerged to provide some organization to the new data. Meanwhile, open notebook science has emerged to open the entire scientific process and practitioners make every stage of research accessible including protocols, raw data, data analysis, and much more open to scrutiny.
Continue reading The entire story of my scientific career
The value of open research
This post is written to supplement the P2PU Open Science Education Module, and in particular is meant to be an introduction to open research education.
My name is Anthony Salvagno and I'm an open notebook scientist. That basically means that I publish ALL of my research in real-time on the web. All of that research is attributed under a Creative Commons Attribution ShareAlike (CC BY-SA) license, so the information is free for anyone to use.
If the foundation of science is the pursuit of knowledge and to share that knowledge, then why is it acceptable for scientists to hide their research? Why is it ok for publishers to make you pay for that information? Why is it scientific culture to protect data like it is a commodity to be sold?
In truth, that system worked in the past because the technology was limited. Now the technology exists to instill a new culture. But what are the driving forces that would push someone to make this change? Simply put, I was fed up!
I was originally pushed into open science for one simple reason: my advisor was trained in an extremely closed system. In my first year of graduate school (and his lab), I was presented with the concept of open science, which then was barely taking hold. I was surprised to learn that scientific culture wasn't a naturally open system, and in fact was surprisingly opposed to that concept.
Early in my graduate program, I became frustrated with the way scientific publications were written. I could only understand a small percentage of the articles I was reading, articles that were written by my peers. I knew most graduate students felt the same way. If we are producing the data and writing the papers, then why would we continue to perpetuate the cycle? So I decided that all of my research would be as accessible as possible.
At times, I would need to understand an experimental process, so I would scan the literature and try to repeat experiments to gain a foothold. I became frustrated with the content contained in the methods sections of scholarly work. Often, the methods would be vague, condensed, or just incomplete, and it would cost me time and money trying and failing to repeat experiments. So I began to document my protocols completely, including minor details that could potentially save other scientists a lot of time.
I have also come across scientific results of a questionable nature. Most of the time the results seemed incongruent with my own research, or even just based on my own expertise I knew there was no way to achieve those results. But the scientific process lacked transparency, so there was no way to understand how the researchers obtained their data. So I made sure that my analysis was entirely transparent, and I provide the data during every phase of analysis including the raw data.
In essence, I have become the scientist that I am because of the experiences that I've had. Instead of perpetuating the problems that exist in modern scholarly work, I work toward making a change.
I know I'm not the only scientist who has come across the same issues, in addition to other ones. There are a lot of open scientists who work toward the same goals. We hope to bring about a new culture to enhance the speed of science, to improve our collective knowledge, and to make discoveries that would be impossible in the old system. That is why open research practices are important to me, and that is why every scientist should be an open scientist.
Patent law and open notebook science
The America Invents Act was initiated in 2011 and institutes some new changes to patent law. The newest inclusion to the law is that now patents are given based on a first-to-file system, whereas previously they were given through a first-to-invent system.
I found out later that this was not true. The speakers confusingly used the terms disclosure and public disclosure, not interchangeably but it seemed that way. See below.
I mention later that public disclosure is called prior art. Under the former system there was a year of protection from the moment of public disclosure prior to filing a patent, as long as you could prove that you are the original inventor. Under the new system there is no longer the first-to-invent policy, so public disclosure could become even more important.
There was the scenario presented with two inventors. Inventor A publicly discloses invention. Inventor B files for patent some time later. Inventor A then files for patent longer than the 1 year grace period for prior art. According to the presenters, neither inventor gets the patent. I didn't understand why.
The pre-filing is what I call provisional application in the next tweet.
According to speakers, the provisional application is low cost ($125 for small entity inventors, such as individuals, $250 for large entities like corporations). The intellectual property is also kept secret during the provisional period until patent. The provisional application provides the inventor with the 1-year grace period that also comes with public disclosure, but you have the ability to maintain the secrecy of your project.
I clear this up in some tweets below.
Statement was made about this giving leverage to corporations with lots of money over individuals with lower financial capabilities. This is why provisional application is a decent work around. Also why open notebook science is an even better work around (free).
Foreign patents and foreign public disclosure count in the US as prior art, and fall into the 1-year grace period. Because this places a new burden on the US patent office, patents may be granted in excess (which is already in excess) and patents may not be invalid until there is a conflict dispute. I'm pretty sure that's how a lot of patent proceedings already occur. This eventually puts the onus on the inventor to find infringements and file suit to argue the point.
The next three tweets are a copy and paste from Wikipedia about prior art terminology.
Prior art and public disclosure are the same thing. And I think the third tweet refers to patents from other entities, not the original inventor.
Looking like #opennotebookscience and #openscience better for filing patents than being secret
This is actually confusing. If you are doing research with a collaborator at another institution/company file a joint research agreement. Neither entity can file a patent first without the other entity. The joint research agreement may/may not act as prior art, I wasn't sure about that one. But the important point is that joint research agreement helps the process.
The speakers gave an example, but the details are fuzzy. They said they would post the slides, so when that happens, I'll share them and refer to the timeline.
Still not sure how #opennotebookscience can be helpful/destructive for patent filings. I've never heard so many contradictory rules!
Based on the presentation and the discussion afterward, open notebook science can actually be beneficial for patent filings. JC Bradley highlights this below, and even with the law change it seems to be even more useful since first-to-file is the crucial step now.
@Thescienceofant here is one way ONS interacts with patent law usefulchem.blogspot.com/201…
That was all I had for the presentation. I spoke with the speakers after the presentation, and asked them about the relevance of ONS to this topic. As I mentioned above, the change from first-to-invent to first-to-file makes it a race to patent. The argument is that entities with a lot of money would benefit since they could just patent every idea. The law is made more accessible because first-to-file can be attributed via a provisional application or public disclosure. From that point on, the applicant has 1 year to file a patent.
To me, open notebook science can be a major benefit to the new patent process. Since it does cost money to file a provisional application, ONS (or other web disclosure) would provide a free alternative to the provisional application. The only difference between the two routes is that through ONS, the patent is immediately public information, while the provisional application keeps the idea in secret. Because the patent will eventually be public domain, the incentive to innovate is delayed a bit.
It should be noted that even though ONS makes your idea open, and encourages potential modification it does not encourage stealing of the idea. You are still protected from patent infringement. But if a competitor sees your idea and makes non-trivial (non-obvious) changes to your idea, then they can be granted a new patent. That is no different from how the patent process works anyways.
But to me, filing a provision for every idea you ever come up with and paying $125 every time is a waste of money since you aren't likely to follow through with every idea. It also gives the US patent office a lot of unnecessary paper work, and could actually stifle innovation and creativity. ONS would in turn allow some one to share their ideas and protect the best ones for the original creator (since you have one year from first disclosure). You could use your resources to fight for the ones you want to keep and allow others to cultivate the ideas that you won't ever get to work towards.
It was interesting that when I asked the speaker about ONS and patents, while he didn't say the conflicted (cause they don't), he did say that it didn't make sense to pursue both paths. His reasoning was basically what I outlined above, but it also felt like there was a money undertone to it. You can't make money if you share your ideas. To that I disagree, but that's an entirely different story altogether. One that I hope to address in April.


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BOSTON (AP) - In the tight Massachusetts Senate race, GOP incumbent Scott Brown has spent weeks questioning Democratic rival Elizabeth Warren's claim of Native American heritage, while Warren portrays Brown as a darling of Wall Street.
The rhetoric is constant, sometimes caustic and all but invisible from the ad campaign waged on television.
That's because Brown and Warren signed a deal to discourage third party groups from running television, radio and online ads in Massachusetts. At this point, at least, their pleas seem to
have been heard and two are leading by example.
In his TV ads, Brown shows himself as a cheerful bipartisan lawmaker, doting father and supportive husband. No mention is made of the issue that's become the near sole focus of his campaign: Warren's flummoxed handling of questions about her heritage.
Warren also has run a tougher campaign off-screen than on.
At campaign stops, she routinely refers to Brown as "Wall Street's favorite senator," a phrase that's absent from her TV ads, which aim to portray her as a fighter for the middle class.
The race is one of the country's most competitive as Democrats look to take back the seat long held by the late Sen. Edward M. Kennedy until Brown shocked the political world by winning it in 2010. Democrats hold a slight edge in the Senate and they see Massachusetts as their top chance to pick up a Republican-held seat to offset any losses they may incur elsewhere.
Yet, so far, Massachusetts voters have been spared the kind of corrosive ads that have flooded the airwaves in Nevada Virginia and other states with hotly contested Senate contests.
Brown and Warren can't stop outside groups from getting involved. But less than five months before the election, it seems those groups are taking the candidates' wishes to heart. If the groups stay on the sidelines, the candidates would have to use their own ads to attack each other, should they decide to go that route.
That poses a particular risk for Brown, who has tailored a good guy image in his ads. The most recent features his wife, former Boston television reporter Gail Huff. Brown also championed the ad deal, saying it would help elevate the political discourse.
John Baick, a professor of history at Western New England University, said that without the agreement, GOP-aligned political action committees already would be targeting Warren with harsh ads.
"I'm sure there are outside conservative groups who are frustrated," Baick said. "They could have an ad on the air in two minutes, but they can't. It's one of those nonissue issues that can play so well."
The dust-up over Warren's claim of Native American heritage surfaced at the end of April when The Boston Herald first reported that Harvard University, where Warren works as a law professor, had touted her as a Native American.
It was later revealed that Warren had listed herself in law school directories as having Native American heritage. She also identified her race as "white" on an employment record at the University of Texas and declined to apply for admission to Rutgers Law School under a program for minority students.
Warren has acknowledged telling Harvard and her previous employer, the University of Pennsylvania, of her Native American heritage, but only after she had been hired by both schools.
Warren, who grew up in Oklahoma, said she and her brothers were told by their parents that her mother was part Native American. She said she never sought proof of her ancestry and her campaign has been unable to verify the claim.
"My mom and dad were deeply in love," Warren said in recent interview with The Associated Press. "My father wanted to marry my mother, his parents objected, because she was part-Cherokee and part-Delaware."
Brown's campaign seized on the issue, arguing that Warren used the claim to gain an unfair advantage inhiring. Harvard Law School professor Charles Fried, a member of the committee that reviewed Warren for a job at the law school, said the subject of her Native American ancestry was never mentioned.
While Brown has steered clear of the issue in his television ads, he's raised it in news releases, during campaign stops and in interviews with the media.


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Wentworth dorm plans OK'd by city
Wentworth Institute of Technology's plans to build a new dormitory on Huntington Avenue have been approved by the city.
The Boston Redevelopment Authority board Thursday unanimously approved Wentworth's proposal to build a 7-story dorm at 525 Huntington Ave.
The 110,760 square-foot building is designed to house 305 students, allowing the school to keep 96 percent of its students living on campus.
The apartment-style units are designed to attract upperclassmen to on-campus housing, according to the project's Facebook page.
The new building will be built on a piece of land at the intersection of Huntington Avenue and Louis Prang Street that has served as a school-owned park. When complete, the building's Huntington Avenue side will host 1,897 square feet of open space near its entry.
The $43 million project will create 275 construction jobs and six permanent jobs, according to the city.
This is the latest expansion the school has taken on in recent years. This fall, the school celebrated the opening of its newly built Center for Sciences and Biomedical Engineering and the William H. Flanagan Campus Center.
Twitter: @YTFenwayKenmore
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(FOX 25 / MyFoxBoston.com) – Parts of the subway system are back up and running, but the transportation system is still a nightmare in New York City, where bus lines wind around city blocks.
The death toll from the super storm is rising and patience is wearing thin.
There are huge challenges ahead for cities trying to recover, including fuel shortages and more than three million customers still without electricity.
You can imagine the frustration with the lines of people in New York City waiting for buses. There are long lines for gas, too - 14 blocksat some stations - easily a mile or more. The Associated Press is reporting a guy in Queens even pulled a gun on someone who complained when he cut the line.
Drivers are being asked to carpool with three or more people to try to cut down traffic.
The backbone of transportation in New York City - the subway system - is showing signs of improvement, but water in the East River's tunnels means only trains above 34th Street are up and running and even those are still on a limited schedule.
Crews from Massachusetts are doing what they can to help. Mass Maritime is reportedly sending a boat to serve as a floating hotel for relief workers.
An 80-member search and rescue team from Massachusetts is working around the clock in New York and New Jersey. On top of all that frustration and so much sadness, the bodies of two little boys were found on Staten Island. A 2-year-old and his 4-year-old brother were on their way to Brooklyn with their mom tried to escape the storm, but rising flood waters forced them onto the roof and the boys were swept away by large waves.
So with all this in mind, there are questions heading into the weekend about the New York Marathon. Many who lost everything and are dealing with no basics like power and water say cancel it. But Mayor Bloomberg is pushing ahead. Marathon organizers tried to curb backlash by launching a program called "The Race to Recover" and putting in $1 million.
What do you think? Should the marathon still go on? Let us know on Twitter and Facebook.
Click here for complete Sandy coverage.
© 2018 Cox Media Group.


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You may have figured out by now that I am a bit of a flower nut (I am only just realizing the extent of it myself). Although the weather has not been great in the Maritimes so far this summer, it has worked out beautifully for me, as I get to experience all the gorgeous blooms of spring all over again! In particular, my parents have two varieties of peonies that are just spectacular. I have no idea what their names are, but the first is a creamy colour, with just a hint of yellow and an incredible scent. The second is this glorious pink and yellow number that has no scent but it one of the most striking flowers I have seen. The fronds inside look like they belong deep in the ocean on a reef with clown fish poking their heads out of them. I do hope you are not sick of my endless flower photos, because here are a few more:
Endless Spring
Labels: flowers, garden, home, New Brunswick, photography, photos
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Wade Waddell and Henry Fernberger, members of the 2013 US Sailing Development Team, come to the 2013 420 Worlds with another year's experience under their belts and the benefit of a seventh place at the ISAF Youths putting them in strong contention for a top ten result in Valencia. The pair made an impression at the 2012 420 Worlds with a 15th place finish on their debut appearance, before accelerating up the leader board to finish sixth at the 2012 420 Junior Europeans a few weeks later.
Africa is fielding three teams at this year's Championship, with Angola in the 420 Open and South Africa in the 420 Ladies. A proud landmark for Angola as the nation realizes its long term goal of competing at the 2013 420 World Championships. It was back in October 2010 that the first 420 Clinic was held in Luanda, Angola and their future sailing ambitions were revealed. Significant resource has since been spent to further develop the sailors, investing in a fleet of twenty brand new 420s and holding follow up clinics, both in Angola and in partnership with the Clube Naval de Cascais in Portugal. It is tremendously exciting that Angola has achieved their goal with two teams, Paulo do Amaral and Leonildo Feliciano along with Manuel Nzuzi and Carlos Fernandes competing. Do Amaral and Feliciano won the Angolan 420 National Championships in March this year, and both teams have been undertaking some intense pre-Championship training in Portugal.
Nuno Gomes from Clube Naval de Luanda, who has been instrumental in the development of sailing and the 420 fleet in Angola, said, 'There has been an intensive sailing development programme over the past six years. Initially it was just the Optimist class, as we didn't have 420 or 470 and just five Vaurien and three Laser. But when the 15-16 years old kids left the Optimists there was a need for other classes to show up and the Angolan Federation, together with Clube Naval de Luanda and Clube Nautico da Ilha de Luanda, invested in twenty 420s, ten 470s and five Lasers in order to promote other dreams - namely our desired Olympic participation.'
On their goals at the 420 Worlds, Gomes continued, 'The teams want to learn as much as possible, get some experience in big international events, have lots of fun and try to win.'
Seventy-seven teams will line up in the two fleets in the 420 Ladies World Championship, with only one of the medallists from 2012 returning in the form of Chile's Nadja Horwitz.
Horwitz and crew Carmina Malsh will certainly be amongst the teams likely to be prominent at the front of the pack along with Italy's Ilaria Paternoster and Benedetta Di Salle. The two have been continuously sparring at the front of the 420 leader board at the major Championships in recent years, and it will be a repeat battle this year.
Horwitz has been on a mission to secure gold at the 420 Ladies Worlds for several years. She safely stepped onto the podium with a silver medal at last year's World Championship in Austria, a rewarding upgrade from a fifth place at the 2011 Worlds in Argentina, and at the recent ISAF Youth Worlds won silver with Malsh, to finish ahead of rivals Paternoster and di Salle who took fourth overall. Paternoster and di Salle won gold at the 2012 ISAF Youths, but couldn't repeat their success at last year's 420 Worlds where they finished fifth. So it looks as though scores are about equal.
The bigger fleets and pressure of the qualification series changes the dynamics of the race, and whilst these two will be amongst the main contenders, Valencia is set to serve up some challenging racing conditions, which could see any number of teams come to the front.
It has been a year of change for the Chilean team as Horwitz explained, 'We had a lot of change this year with a new coach at the federation and new team work. I have had three different coaches and a new crew who was previously sailing a Laser. Since last year, I am not sure if 'improve' is the word but we have been working hard. We weren't expecting anything at the ISAF Youth Worlds, and found out that we weren't that bad'
A baptism of fire for Carmina Malsh who until arriving in Cyprus for the ISAF Youth Worlds had not been to Europe or competed at such a high level. Horwitz is aiming high on her expectations for the 420 Worlds, explaining, 'Maybe at the Worlds we will try to do the best again and see how it works out. Top 10 and maybe top five. We haven't trained yet in Valencia, if it gets windy we will just have to get out and see how it works. We are ready for everything.'
Spain is fielding 14 teams in the Ladies Worlds including Silvia Mas and Nurio Miro who finished fifth at the ISAF Youths, and only seven points off the bronze medal. They have had a great year so far, including a third at the Spanish 420 National Championships in an open fleet and, with the added boost of sailing at home, this pair are likely to be on a roll in Valencia.
Moving to Asia and Singapore's Kimberly Lim and Savannah Siew were the top placed crew in the under-16 division at the 2012 Worlds, finishing in fourth overall. They are also veterans of the ISAF Youth Worlds, finishing fourth this year and ninth in 2012, so plenty of experience behind them. Lim hit the world sailing stage big time in 2011 when she was crowned Optimist World Champion – so expect something special from this pair.
Another nation fielding a full seven teams in the Ladies Worlds is Japan, up from a single team in 2012, notably reinforcing the commitment Japan has made to the 420 as the nation's only recognized junior two-person Event website