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.