Labstyles of the poor and published...

Eppendork has been reassured that the universe wants her to stay in science - my rocky road muffins turned out to be the bomb, also my recipe for raspberry coconut ice muffins is rocking along - like recipes for media it needs to be tweaked but tastes good nontheless. Just so you know the muffins weren't the sign - it was more of the fact I had two job interviews - one for major league university - the main investigator contacted me in person to turn me down - but I was okay with that cause he said I was impressive (it's the small things I know) but the competition was fierce. I like that Im fierce too - followed up by another interview for a job that I thought I had little chance of getting but hear I am happy to say I am employed - it's a short term contract but Im okay with that.

So back to the real world of champagne wishes and caviar dreams and I am really, really happy about it.

That's all.

E.

I has surfaced...

Hello faithful readers - I have been a very lax sci blogger. In fact, some would say I had fallen off the face of the earth since August. Well for all intents and purposes I had, I consider it a well need vaykay or more accurately post stress funk, truely considered walking away from science as my psyche and ego had taken a bit of a battering, but I bend I don't break. This time it was was an extended held pose, consequently I am well stretched and have started applying for jobs again in the science field of mine - some not. Just thought I would let you all know I am alive and am doggy paddling again.

Just to keep you remembering how cool science is - it even does christmas:

Paediatr Anaesth. 2004 Dec;14(12):1016-20.

A Christmas tree in the larynx.

Philip J, Bresnihan M, Chambers N.

Department of Anaesthesia and Department of Ear, Nose and Throat, Princess Margaret Children's Hospital, Perth, WA, Australia. jennyphilip@hotmail.com

A 2 year-old boy presented with acute upper airway obstruction following a 15-month history of noisy breathing and hoarseness. An urgent laryngotracheal bronchoscopy was performed following inhalational induction of anesthesia. Using a fiberoptic bronchoscope, visualization of the larynx through a laryngeal mask airway revealed a flat plastic Christmas tree embedded within granulomatous cords causing almost complete obstruction and requiring tracheostomy prior to extraction. Twelve days later, the tracheostomy was successfully decannulated with the child's voice beginning to normalize. The family remembered the decoration from Christmas celebrations 2 years prior and recalled a coughing episode that predated the onset of hoarseness.

You gotta love it.

E.

You know I loves Science

but I just don't love scientists (well that's a sweeping generalisation) but flow with me here.  Officially Eppendork doesn't love hates a system that tolerates unprofessional behaviour because you are a leader in your field and you bring in the big bucks.   My supervisor is a great scientist (I completely respect his science) but his managerial skills are absolute crap, and if I had to I would say they are non-existent.   I have never ever been managed so badly by a supervisor, never.  Nor have I ever been so stressed out and paranoid about making mistakes as I have been in the past few months, I have been a complete fking wreck (hence the lack of blogging).  He just has no stop measure on his temper - there is a zero to 100 in terms of anger in like 5 seconds and just lets rip on the person - alone, in front of people, in front invited guests.  He just doesnt give a shit and everyone takes it because with his name on a paper you are going to get it published in one of the big ones.    He is a micromanager, in and out, in and out - unless he has some one else distracting him that he can 'help' them see the error of their ways (cause they arent thinking just like him), you never get time to do stuff and he continually adds things to your list of stuff to do.

I have been contemplating in the last week or two whether he is a workplace bully or he is just insensitive to the dignity of others, and to be honest I think it's the later and has no control over his temper.  He had threatened me twice with being 'fired' from this PhD project - the first time was like - OMG he's threatening me - WTF?? This was after he and my other supervisor had a meeting and worked out a plan for me to improve my performance to be reviewed in three months at which point we as a group would decide if this project was to go forward.  The last time he told me 'you dont know how close you are to being fired!' and in my head I was just like - meh if you are going to do it, do it (the reader must realise at this point I had got my head around the fact that he and i shouldnt be working together cause we are a really bad fit) I dont care that much.  But I still thought I had my now two months to prove myself worthy of his godlike tuterage, unfortunately this morning he had decided he had enough and told me I was fired from the project.  And you know what (having spent my weekend working my arse off for him) just sat there and went thank fucking God - thank you Jesus.   It had been taken out of my hands and I am glad cause me being stubborn and not wanting to give up on something until the last possible moment would have sat there a stressed out, wreck of a person, a shell of the person I walked in here as and I can tell you I would have lost my love of science.  It was ridiculous how much lighter I felt walking back into my office - one of them (who is in my office but not in the group but see how he behaves to all of us) - was like 'Oh Eppendork I am so happy for you - this is a really, really good thing!'.   Every one including the tech who is also leaving soon because of his behaviour (although she gave him another reason cause she needs a good reference), was like it is a positive positive thing.

And dear readers it is!  It really, really is!  Just have to go find me another job and explain why I spent x amount of time on a PhD project that has come to nothing - but I can live with that, I still love science and tonight Im not a wreck!!  I might just sleep soundly for the first time in months as well....

Hallelujah, Hallelujah, Hallelujah.

E

xxx

Eppendork's terrible, horrible, no good, very bad six months

I confess I have a problem. It is all to do with my love of praise and dislike of disappointing people and feeling like a failure. I have spent the last six months spending more of my time feeling like I am dog paddling in the pool of wanton science dreams. Yep you heard floating/dog paddling and not swimming and I am getting tired. I desperately want to get my shit together and I am hoping my research proposal will meet with supervisor A and supervisor B's approval so that i can get my shit together. My manic depressive relatonship with supervisor A is not helping my balance - he is a really high achieving and extremely well respected in our field (which makes lit reviews fun when he's on half the papers you are talking about), he has high expectations of all his staff and students and gets all disappointed (verbalises this both in front of other people and has been known to lose his temper at people in front of people even at visiting students - which reduces you and whoever else is around to feeling super duper crap). He does give you praise and its honest not manipulative praise - when i get it im like omg the world is brighter, better more fabulous place and then in the next breath he will go 'I'm disappointed' or I dont have time for this go away and do it again (tbh some of the time its me thats cocked up - but more often he changes his mind about what he wants after I spend ages on it and I have to do it again. Or he just doesnt listen and you have to push the point and make him hear you or he will walk all over you with his assumptions.  I made a choice I chose this project this supervisor go me!

Having said that i love this field, I love the kind of work I am and have been doing. I am not stupid. I will resolve it. I just need a really big wine right now. Tommorrow is a new day - I have a project proposal to work on and hopefully they will buy it and not throw me out on my ear.

E.

Be scared, be very scared and dont fall asleep!

Get Your Cyborg Name

Heehehe - eat my cyborg dust science!

That is all.

E

Everybody say Yey-ah! Yey-ah!

I got the script to work :-p which is good and maybe i will share with you maybe I wont in the future - probably will! But then in future planning will remember about the primary key needing to be the same as the key you want to join the tables with :-p but i think that is relatively easily solved I think a new_list.remove will work - let us all cross our fingers and tune in next time for when we hear Eppendork say Yey-yah! uhuh! Yey-yah!

E.

Calling all Pythonistas!

Okay so I have a question:

I have a pile of sequences (200+) in fasta format in a text file eg 

>geneA

asdfdfasfsdfasdfsdfsdfsfdsfsdfsdfsdfasdfsdfsdfasdfasfsdfafasdfsdsdfsfs

afasdfasdfasdfsdfasdfdfafdasdfsdfafasdfasfafdsfasfafsdfsdfasfsfasdfsdf

>geneB

asdfdfasfsdfasdfsdfsdfsfdsfsdfsdfsdfasdfsdfsdfasdfasfsdfafasdfsdsdfsfs

afasdfasdfasdfsdfasdfdfafdasdfsdfafasdfasfafdsfasfafsdfsdfasfsfasdfsdf

>geneC

asdfdfasfsdfasdfsdfsdfsfdsfsdfsdfsdfasdfsdfsdfasdfasfsdfafasdfsdsdfsfs

afasdfasdfasdfsdfasdfdfafdasdfsdfafasdfasfafdsfasfafsdfsdfasfsfasdfsdf

I need to make it into columns like this:

geneA asdfsdfasdfsdfsdfsdfasdfsfasdfsdfafsdfsdfasdfasdfsdfasdfs

geneB asdfsdfasdfsdfsdfsdfasdfsfasdfsdfafsdfsdfasdfasdfsdfasdfs

geneC asdfsdfasdfsdfsdfsdfasdfsfasdfsdfafsdfsdfasdfasdfsdfasdfs

all in one line.  I want to have the text file set up like this because i want to use python to stuff the text file into an SQL table - only I dont know how to do it - I can concatenate the sequence bit of it in excel for one of the sequences but that doesnt work for the 200+ other sequences I have.  Everything I have found on fasta and or concatenation involves simple exercises or pulling down individual fasta sequences from genbank which didnt help me a lot.

So what I want to know is how do i get the sequence name in one column and all sequences in the other so that I can make an output file that I can open using a python script then stuff into an SQL table.  Any ideas?

E.

It's a good day today

I feel slightly like I have a manic-depressive relationship with my supervisor.  One its good and he's happy and all is right with my world (sometimes I feel really good).  Then the next day he will just be tearing strips off me and handing my arse to me on a plate and I feel like what the hell was I thinking doing a Phd.   Kinda like this:

SELECT * FROM "Eppendork"

WHERE "EmotionalState" LIKE  'F%'

ORDER BY "Dayoftheweek" 

AND "Houroftheday"

Which roughly would give you the hours and days of the week where I felt F**d or Fabulous. Yes this week has been good for SQL and me making a start on learning Python.  I got excited today by:

n = int(raw_input('What's my favourite number?: '))

if x >4:

print 'No that is not my favourite number!'

elif x<4:

print 'No that is not my favourite number!'

else:

print 'Yes that is my favourite number! Woot!'

I know baby steps - its the small things.

E.

Reality sux, but in the meantime I have Chilli-tomato lentils

So I have been burying myself in my literature review basically to distract myself and avoiding the very real family crisis that is going on at the moment - given I am far, far away and feeling a little helpless.  My mum has been told that her heart is so badly traumatised by her congestive heart failure (not to mention al the other things) that they cant replace the pacemaker that is currently failing - she wont survive any type of surgery and they basically they have sent her home with the expectation that she wont see out the year.  So Im gutted.  My supervisor has been good and said I can take time off to go home - but I need to time it right given I cant afford to make the trip more than once.  I was trying distraction but apparently not that well.

So I was head down bum up trying really hard to focus on the lit review - but with the help of a friend realised that to a large extent what i was writing was skimming the surface, trying to cover too much and not enough detail.  It also hasnt been any near where the level of my writing usually is - so it is in other words crap! So i have set it aside and made up a new plan of attack hopefully supervisor will agree to it.  Starting next week after an intensive programming course which I had asked for earlier prior to the current goings on but I need to get my shit together and get things done - focus Eppendork - focus!  But it's hard.

E.

And on and on and on and on and on infinitum

Notice no fullstop at the end of infinitum because although you can get to the end of the word infinitum the concept itself just goes on and on and on and on and on. Much like lit review writing, thesis writing and the writing of those loverly journal articles we all like to prize above all else epeshially if they manage to get snagged by the she daddies of the science world in terms of journals. Eppendork is not so lucky. Although she has two more articles out of her MSc .than previously (they are still in the process - one in press the other submitted) neither of them will be submitted to the double mecca of dynastic scitholicism, just plain ole respectabible journals that dont do the bells and whistles and pretty sequins. No, no she is currently writing for a lit review and my what fun she is having - gee if i had known it would all be picnics and fuzzie bunnies I would have done this sooner!

Figure: I love this cartoon - it just makes me laugh!

Note to self: sarcasm may go over heads of readers - I don't think its fluffy bunnies at all and if the weather would just stay sunny for a while it may be picnic weather. It's Saturday and I have been head down bum up for way longer than I care to admit - and I may be just procrastinating now and yes, yes I am procrastinating. Rather I am giving the brain a little rest and I will be back into it asap because really chickens I do see the light at the end of the tunnel today - didn't yesterday - its babysteps.

E.

Pink No More

Tired of gingham - so March!  I am had long day at the Biosafety cabinet chickens so Eppendork is tired and thought about Abel Pharmboy's little titilating rant about vaccintions and sexy, sexy videos.  I was going to have a rant balanced discussion about the pro's and con's of vaccinating your beautiful children - very little con's lots of pro's to be very honest and how more discussion and talking with people who don't have 7 year degrees is a good thing (and I realise here that saying if you have Phd or a MD you are going to vaccinate your child is not always true but more likely I think if the PhD is in some form of Science).   How ever I don't think it matters how much we the microbiologists, the medical plethora and other scientists say vaccinate your child those who really dont want to aren't going to. Which saddens me but not a lot you can do about it.  I still think it does border on child abuse - when a disease is preventable it should be prevented.  Fullstop.  End of story.  If you want a nice discussion about how vaccines work ToasterSunshine has one.  I am just too sleepy.

E.

I wonder

I wonder if the person giving a presentation on their past year or two's work should feel insulted that a lead PI nodded off during their presentation? What do you think?

Eppendork may have a little crush on Mr Nick Cave

I love this song - PJ Harvey rocks the house too.

I am up to eyeballs in Lit review at mo - so not too much blogging going on unfortunately.

E.

PS fave Nick Cave song - Into my arms - seriously good song - the man's a genius.

On why Macs rock da hizzle

I Eppendork own a Mac - it's true.  I haven't always been a fan Mac's used to be very naf and then one day they weren't they were sexy and sleek and did all sorts of hot funky things and the whole no virus thing is da bomb, well the world was mac's oyster.  With itunes/ipod, iphone and beautiful Mac laptops well they can do no wrong really.   There is even a documentary about people who love their Macs. Now the iphone is truely an ass kicking hot piece of technology - it is just that sexy - love playing with it a lot.   I havent manned up and brought one yet but I know some one who has one and they let me play with it if I'm good.   The reason for this little ramble into Eppendork's sometimes mac fetish was this little slide show in the New York Times - what to do when you have too much time on your hands.

Figure 1: Ooooosh!  

Ask me again why I think Mac's are da bomb - they're like little cockroaches of the computer world...

E.

I'm so sick

So sick that I wrote sik three times before I could get the word spelt properly.  I wanna bitch about American Idol - are you all so stupid that if they tie them up with a bow they're gonna make it in the fickle, fickle world out there?  Removing anyone of any real interest - bar the guy with the indie bent - makes AI a dull show - cookie cutter molds are destined to fail - cause the flavour is going to change and no one wants your gingernuts any more.  And really why isnt there a Science Idol - hmmm?  Well I realise there is the Nobel prize but thats for people who have been there done that a lot - kinda the point of the prize.  Seriously, where is the competition for noobs who have talent but just lacked their 'big break' - huh?  

I may need some more flu meds.  

E. 

The Leslie Winkle experimental methodology

Okay so as I write this I am tucked up in bed with the flu, I have my lemon, honey and ginger tea next to me, on the other side is the work I brought home with me that I have yet to pick up yet.  Very hard script is on top of the pile mocking me with its brilliance - I made a little progress on understanding it - upside is I have realised I will have to learn how to script in python - although I am told once I know how to script in it - I wont ever go back - bit like the dark side really.  Any who I was reading Juniper's blog, about her current trevails and trials in her pathway to become a real scientist, and I thought to myself damn - how can it be so hard?   Then as I do in my slightly drug-induced fluey state I thought - things happen for a reason and sometimes we dont get what that reason is until we get to a place where we do.   

For me I wanted to do science when I left high school - but due to a mixture of severe lack of intellectual self esteem and generally propensity to take the easy way out (when I was 17) I enrolled and completed a very average BA and then took up the only career I believed was open to me.   Turned out I was good at it but I felt like my true potential was being smothered and I just couldnt do it anymore - so I stepped outta my comfort zone a long way outta my comfort zone and found the confidence to do what I wanted to do in the first place, science.  I thought of doing medicine so I started there and my undergrad was focussed on that goal - but in the end I decided Micro was where it was at and battabingbattaboom whaddya know here I am.

Course it didnt happen all nice and neat like that - when I said I wanted to do science, my then partner basically laughed and fully expected me to fall flat on my face and go back to doing what I did before within a year of starting my undergrad.  It felt good to show him the straight A's I got in my first year - I didnt give up I worked two part time jobs and was a full time student and a mother.  It wasnt easy and I have to say the first year of my MSc was the most stressful year I have ever experienced in my whole life - I wouldve lost the plot completely had it not been for a very good friend of mine who I love dearly.  Needless to say my relationship with my ex didnt last, but my relationship with science is still going strong.   When I think about it now - if I had of tried to do my science straight out of high school I would have crashed and burned majorly - I didnt have the motivation or the self confidence to do the work that had to be done.  I couldn't see that at the time.  I do now - I had to go through a shit load of growing up to realise I had a brain in my head was useful for something other than sleeping and breathing.

Juniper sweet cheeks - I almost feel like you need to take a time out and center yourself and make a plan.  OMG I am such a control freak - I am such a planner - I like to know what to expect - go figure.   You need to focus your efforts, don't disperse them left right and center - get a piece of paper out - write down what you want, what you want to do and how you are going to get there.  Find places that are doing what you want to do - then ring them up and explain your situation - could you intern for them? Could you do an MSc with them?  You never know your luck - and believe that half of the science opportunities start because some is in the right place at the right time.   You are a kick ass writer - your blog shows that - figure out what you want to happen and then make it happen - you are the only person who can do it for yourself and you are the only person who can stand in your own way.  Focus chick focus.

E.

PS:  Still fluey  gotta love viruses - they are little pieces of God's own glory they are, they are.  Mmmmm I have M&M's as well - purely for medicinal purposes you understand.  

Old Skool Styles

Vintage just says Im Styling hot Science Chick - dont make me take off my sunnies and come over there!

So I took a facebook quiz to burn a little time - Eppendork decided that if Isis can blog about Barbie then I can certainly take a quiz to find out just what sort of Barbie I am.  So I took it and the news is out - Eppendork is old skool - Vintage Barbie - classic down to her mean patent pumps and kick ass corset figure.  Did I mention I have a slight girl crush on Ms Von Teese?  I wish I looked that good!

That is all.

E.

A good use of Resources - Methinks

So trawling through the internet one fine day - I found this:



Not for the squeamish - forewarned is forearmed. Couldn't do it these days....

E.

I'm out and I'm proud

Hello my name is Eppendork and I write a pseudononymous sci-curious blog.  I started this as a way for me to blog about (crap) important stuff that was going on in my search for just the right kind of scientist I wish-hope-wanna be.  Little did I know I would find out that I had a latent talent girls and boys - not hula hoop dancing, not how many M&M's could possibly fit in your mouth should you ever try, not intuitively knowing Gregory House style that the cat likes the warmth feverishly dying people give off.  No darlingks I Eppendork - Current Queen of the Pink Gingham - have (Eppendork hangs her head - sigh) an apparent latent talent for writing scripts - computer program scripts - not pharmaceutical scripts before you get excited.  

Figure 1: Yes, Eppendork does look this hot, but will try hard in the future not to search for hot geek girl or eve comp geek girl in Google.

I wrote my first real script today that actually did something useful rather than "Hello World" or similar.  It was a short little script and it really only changed a few things in the database but it saved me work and I wasn't expecting to feel proud of myself for doing it - but I did (blush).    I kinda feel like scripting will save a shedload of time and effort in taking care of my db's (eww listen to me db's) in the future.    

E.

Open Letter to Adobe

Dear Creators of Adobe Illustrator,

I am a great fan of Adobe - where would be without our faithful versions of journal articles?  I for one am really, really grateful - I love my interesting reading and pretty, pretty pictures therein associated with said articles.  However, Eppendork is not a computer geek - although evidence to the contrary (learning various scripting languages should not be taken as evidence of the former), and finds programmes such as Illustrator very cool, just not very intuitive at all.  

Figure 1: Any of these geeks will do - I am sure the Apple guy will know!

I spent an hour and a half this morning trying to figure out how to import a picture and then recolour it - figured the first bit out pretty quick - the rest of the time to figure out the later.  Sufficient to say Eppendork is not stupid - just hasn't worked with your program before.  I would be completely in your debt if your computer savvy boffins could figure it out for me and other non-computer geeks. 

Luv and Hugs,

Eppendork.